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master vs. PR #3881: `-v 1` vs `-v 0`

Created 2 years agoDiff never expires

##[debug]Evaluating condition for step: 'Run batch_processing.sh'

##[debug]Evaluating: success()

##[debug]Evaluating success:

##[debug]=> true

##[debug]Result: true

##[debug]Starting: Run batch_processing.sh

##[debug]Loading inputs

##[debug]Loading env

Run bash batch_processing.sh

##[debug]Overwrite 'shell' base on job defaults.

##[debug]/usr/bin/bash --noprofile --norc -e -o pipefail /home/runner/work/_temp/f60e562d-3117-4569-b195-998c6fbd3e40.sh

##[debug]/usr/bin/bash --noprofile --norc -e -o pipefail /home/runner/work/_temp/15d4fe95-291b-4e49-89f7-372914cddae6.sh

# For full verbose, uncomment the next line

# set -x

# Fetch OS type

if uname -a | grep -i darwin > /dev/null 2>&1; then

# OSX

open_command="open"

elif uname -a | grep -i linux > /dev/null 2>&1; then

# Linux

open_command="xdg-open"

# Check if users wants to use his own data

if [[ -z "$SCT_BP_DOWNLOAD" ]]; then

SCT_BP_DOWNLOAD=1

# QC folder

if [[ -z "$SCT_BP_QC_FOLDER" ]]; then

SCT_BP_QC_FOLDER=`pwd`/"qc_example_data"

# Remove QC folder

if [ -z "$SCT_BP_NO_REMOVE_QC" -a -d "$SCT_BP_QC_FOLDER" ]; then

echo "Removing $SCT_BP_QC_FOLDER folder."

rm -rf "$SCT_BP_QC_FOLDER"

# get starting time:

start=`date +%s`

# download example data

if [[ "$SCT_BP_DOWNLOAD" == "1" ]]; then

sct_download_data -d sct_example_data

Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_download_data -d sct_example_data

Trying URL: https://github.com/spinalcordtoolbox/sct_example_data/releases/download/r20180525/20180525_sct_example_data.zip

Downloading: 20180525_sct_example_data.zip

Creating temporary folder (/tmp/sct-20220920171305.527191-2x2t1fb1)

Creating temporary folder (/tmp/sct-20220921125334.279878-8kt90_xz)

Unzip data to: /tmp/sct-20220920171305.527191-2x2t1fb1

Unzip data to: /tmp/sct-20220921125334.279878-8kt90_xz

Copying data to: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data

Removing temporary folders...

Done!

cd data/sct_example_data

# t2

# ===========================================================================================

cd t2

# Segment spinal cord

sct_deepseg_sc -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_sc -i t2.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data

Config deepseg_sc:

Centerline algorithm: svm

Brain in image: True

Kernel dimension: 2d

Contrast: t2

Threshold: 0.7

Creating temporary folder (/tmp/sct-20220920171307.373406-pm6k_6pk)

Creating temporary folder (/tmp/sct-20220921125336.147834-szwr7fof)

Reorient the image to RPI, if necessary...

Finding the spinal cord centerline...

Creating temporary folder (/tmp/sct-20220920171318.141827-cb7xmz7v)

Creating temporary folder (/tmp/sct-20220921125346.709574-10y6ss9j)

Remove temporary files...

rm -rf /tmp/sct-20220920171318.141827-cb7xmz7v

rm -rf /tmp/sct-20220921125346.709574-10y6ss9j

Cropping the image around the spinal cord...

Normalizing the intensity...

Segmenting the spinal cord using deep learning on 2D patches...

Reassembling the image...

Resampling the segmentation to the native image resolution using linear interpolation...

Binarizing the resampled segmentation...

Removing small objects above slice #240

Found isolated voxels on slice 0, Removing them

Remove temporary files...

rm -rf /tmp/sct-20220920171307.373406-pm6k_6pk

rm -rf /tmp/sct-20220921125336.147834-szwr7fof

*** Generate Quality Control (QC) html report ***

Resample images to 0.6x0.6 mm

QcImage: layout with Axial slice

Compute center of mass at each slice

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_deepseg_sc/2022_09_20_171335.519968/bkg_img.png

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_deepseg_sc/2022_09_21_125404.933067/bkg_img.png

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/style.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars

for dir in range(input.ndim)]

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/main.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/animation.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/yaml.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/filesaver.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/f-icon.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyright.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keydown.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyup.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts

cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts

Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171335.519968.json

Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125404.933067.json

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars

for dir in range(input.ndim)]

To see the results in a browser, type:

xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Tips: If you are not satisfied with the results you can try with another algorithm:

# sct_propseg -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

# Vertebral labeling

# Tips: for manual initialization of labeling by clicking at disc C2-C3, use flag -initc2

sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data

Creating temporary folder (/tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx)

Creating temporary folder (/tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg)

Copying input data to tmp folder...

Straighten spinal cord...

Creating temporary folder (/tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3)

Creating temporary folder (/tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz)

Copy files to tmp folder...

Fitting centerline using B-spline approximation

Error on approximation = 1.45 mm

Error on approximation = 0.8 mm

Error on approximation = 0.78 mm

Error on approximation = 0.26 mm

Error on approximation = 0.18 mm

Error on approximation = 0.17 mm

Error on approximation = 0.19 mm

Create the straight space and the safe zone

Length of spinal cord: 195.1824594930412

Size of spinal cord in z direction: 191.2181565315654

Ratio length/size: 1.0207318333854003

Safe zone boundaries (curved space): [-122.38013064855659, 68.83802588300883]

Safe zone boundaries (straight space): [-124.36228212929447, 70.82017736374672]

Pad input volume to account for spinal cord length...

Time to generate centerline: 22.0 ms

Warping field generated: tmp.curve2straight.nii.gz

Warping field generated: tmp.straight2curve.nii.gz

Apply transformation to input image...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3

Generate output files...

mv /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz

mv /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz

File created: ./warp_curve2straight.nii.gz

mv /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz

mv /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz

File created: ./warp_straight2curve.nii.gz

cp /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz

cp /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz

File created: ./data_straight.nii

Remove temporary files...

rm -rf /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3

rm -rf /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz

Resample to 0.5mm isotropic...

load data...

Apply straightening to segmentation...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -o segmentation_straight.nii -t warp_curve2straight.nii.gz -r data_straightr.nii -n Linear # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

File /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/segmentation_straight.nii already exists. Will overwrite it.

File /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/segmentation_straight.nii already exists. Will overwrite it.

Create label to identify disc...

Creating temporary folder...

Creating temporary folder (/tmp/sct-20220920171418.335766-17xtra4m)

Creating temporary folder (/tmp/sct-20220921125447.708364-pjxkarw0)

Run C2-C3 detector...

C2-C3 detected...

Remove temporary files...

rm -rf /tmp/sct-20220920171418.335766-17xtra4m

rm -rf /tmp/sct-20220921125447.708364-pjxkarw0

File /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/labelz.nii.gz already exists. Will overwrite it.

File /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/labelz.nii.gz already exists. Will overwrite it.

And apply straightening to label...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -o labelz_straight.nii.gz -t warp_curve2straight.nii.gz -r data_straightr.nii -n NearestNeighbor # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

Get z and disc values from straight label...

.. [308, 3]

Look for template...

Path template: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50

Open template and vertebral levels...

Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]

Z-values for each disc: [963, 938, 907, 870, 833, 800, 769, 735, 692, 646, 600, 551, 500, 449, 396, 342, 289, 231, 168, 104, 79]

Distances between discs (in voxel): [25.0, 31.0, 37.0, 37.0, 33.0, 31.0, 34.0, 43.0, 46.0, 46.0, 49.0, 51.0, 51.0, 53.0, 54.0, 53.0, 58.0, 63.0, 64.0, 25.0]

Detect intervertebral discs...

Current disc: 2 (z=308). Direction: superior

.. Peak found: z=-2 (correlation = 0.5785475132964076)

Current disc: 1 (z=337). Direction: superior

.. correcting factor: 1.0

.. Switching to inferior direction.

Current disc: 3 (z=271). Direction: inferior

.. Peak found: z=-2 (correlation = 0.46669793555686756)

.. correcting factor: 1.0

Current disc: 4 (z=232). Direction: inferior

.. Peak found: z=0 (correlation = 0.4759131092619541)

.. correcting factor: 1.0

Current disc: 5 (z=199). Direction: inferior

.. Peak found: z=1 (correlation = 0.5489915159060484)

.. correcting factor: 0.9924242424242424

Current disc: 6 (z=169). Direction: inferior

.. Peak found: z=-1 (correlation = 0.6413729873029947)

.. correcting factor: 1.0003910068426198

Current disc: 7 (z=134). Direction: inferior

.. Peak found: z=3 (correlation = 0.49551596833735867)

.. correcting factor: 0.9856199566825753

Current disc: 8 (z=95). Direction: inferior

.. Peak found: z=2 (correlation = 0.5102032109234909)

.. correcting factor: 0.9777074711764266

Current disc: 9 (z=52). Direction: inferior

.. Peak found: z=2 (correlation = 0.5204922661088763)

.. correcting factor: 0.9723418633663299

Current disc: 10 (z=9). Direction: inferior

.. Peak found: z=6 (correlation = 0.5201107394731823)

.. correcting factor: 0.9585067770985733

Adding top disc based on adjusted template distance: #0

.. approximate distance: 24

Un-straighten labeling...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -o segmentation_labeled.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

Cleaning labeled segmentation:

removing labeled voxels outside segmentation...

Done cleaning.

File /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/segmentation_labeled.nii already exists. Will overwrite it.

File /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/segmentation_labeled.nii already exists. Will overwrite it.

Label discs...

Un-straighten labeled discs...

Parse list of warping fields...

Get dimensions of data...

101 x 139 x 392 x 1

Apply transformation...

Dilate labels before warping...

Creating temporary folder (/tmp/sct-20220920171426.359163-apply_transfo-6bexaavh)

Creating temporary folder (/tmp/sct-20220921125455.872708-apply_transfo-9g92khug)

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125455.872708-apply_transfo-9g92khug/dilated_data.nii -o segmentation_labeled_disc.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg

Apply transformation and resample to destination space...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920171426.359163-apply_transfo-6bexaavh/dilated_data.nii -o segmentation_labeled_disc.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

Copy affine matrix from destination space to make sure qform/sform are the same.

Take the center of mass of each registered dilated labels...

File segmentation_labeled_disc.nii already exists. Will overwrite it.

Remove temporary files...

rm -rf /tmp/sct-20220920171426.359163-apply_transfo-6bexaavh

Generate output files...

File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_seg_labeled.nii.gz

File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_seg_labeled_discs.nii.gz

mv /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/warp_curve2straight.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_curve2straight.nii.gz

mv /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/warp_curve2straight.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_curve2straight.nii.gz

File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_curve2straight.nii.gz

mv /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/warp_straight2curve.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_straight2curve.nii.gz

mv /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/warp_straight2curve.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_straight2curve.nii.gz

File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_straight2curve.nii.gz

mv /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/straight_ref.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/straight_ref.nii.gz

mv /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/straight_ref.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/straight_ref.nii.gz

File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/straight_ref.nii.gz

Remove temporary files...

rm -rf /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

rm -rf /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg

*** Generate Quality Control (QC) html report ***

Resample images to NonexNone mm

QcImage: layout with Sagittal slice

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_label_vertebrae/2022_09_20_171431.921075/bkg_img.png

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_label_vertebrae/2022_09_21_125501.394177/bkg_img.png

Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171431.921075.json

Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125501.394177.json

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/math.py:113: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0. Please use `footprint` instead.

return dilation(data, selem=_get_selem(shape, size, dim), out=None)

To see the results in a browser, type:

return dilation(data, selem=_get_selem(shape, size, dim), out=None)

To see the results in a browser, type:

xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Create labels at in the cord at C2 and C5 mid-vertebral levels

sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 2,5 -o labels_vert.nii.gz

Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 2,5 -o labels_vert.nii.gz

Generating output files...

# Tips: you can also create labels manually using:

# sct_label_utils -i t2.nii.gz -create-viewer 2,5 -o labels_vert.nii.gz

# Register to template

sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels_vert.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels_vert.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data

Check template files...

OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz

OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz

OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz

Check parameters:

Data: t2.nii.gz

Landmarks: labels_vert.nii.gz

Segmentation: t2_seg.nii.gz

Path template: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50

Remove temp files: 1

Check input labels...

Creating temporary folder (/tmp/sct-20220920171437.034485-register_to_template-gbfw5k06)

Creating temporary folder (/tmp/sct-20220921125506.526801-register_to_template-vn_57a1w)

Copying input data to tmp folder and convert to nii...

Generate labels from template vertebral labeling

Check if provided labels are available in the template

Binarize segmentation

Resample data to 1mm isotropic...

load data...

To avoid intensity overflow due to convertion to +uint8+, intensity will be rescaled to the maximum quantization scale

Change orientation of input images to RPI...

Straighten the spinal cord using centerline/segmentation...

Creating temporary folder (/tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps)

Creating temporary folder (/tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3)

Copy files to tmp folder...

Create the straight space and the safe zone

Length of spinal cord: 194.86777391248705

Size of spinal cord in z direction: 191.01429026627324

Ratio length/size: 1.0201737976820586

Safe zone boundaries (curved space): [-122.3822868551715, 68.63200341110175]

Safe zone boundaries (straight space): [-124.3090286782784, 70.55874523420866]

Pad input volume to account for spinal cord length...

Time to generate centerline: 18.0 ms

Warping field generated: tmp.curve2straight.nii.gz

Warping field generated: tmp.straight2curve.nii.gz

Apply transformation to input image...

Generate output files...

mv /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz

mv /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz

File created: ./warp_curve2straight.nii.gz

mv /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz

mv /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz

File created: ./warp_straight2curve.nii.gz

cp /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz

cp /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz

mv /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.anat_rigid_warp.nii.gz /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop_straight.nii.gz

mv /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.anat_rigid_warp.nii.gz /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straight.nii.gz

File created: /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop_straight.nii.gz

File created: /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straight.nii.gz

Remove temporary files...

rm -rf /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps

rm -rf /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Remove unused label on template. Keep only label present in the input label image...

File template_label_body.nii.gz already exists. Will overwrite it.

Dilating input labels using 3vox ball radius

Apply straightening to labels...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/label_projected_1mm_rpi_dilate.nii.gz -o /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/label_projected_1mm_rpi_dilate_straight.nii.gz -t warp_curve2straight.nii.gz -r /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Parse list of warping fields...

Get dimensions of data...

51 x 256 x 256 x 1

Apply transformation...

Apply transformation and resample to destination space...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/label_projected_1mm_rpi_dilate.nii.gz -o /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/label_projected_1mm_rpi_dilate_straight.nii.gz -t warp_curve2straight.nii.gz -r /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

Copy affine matrix from destination space to make sure qform/sform are the same.

Estimate transformation for step #0...

Labels src: [[-0.49785977044107455, -12.840075485893843, 35.579769644543646], [-1.868628377073808, -13.049818470161009, -17.3863725163054]]

Labels dest: [[-0.0, 46.220001220703125, -100.34002685546875], [-0.0, 45.720001220703125, -153.34002685546875]]

Degrees of freedom (dof): Tx_Ty_Tz_Sz

Optimization terminated successfully.

Current function value: 0.981628

Iterations: 2

Function evaluations: 151

Matrix:

[[ 1. 0. 0.]

[ 0. 1. 0.]

[-0. 0. 1.]]

Center:

[ 0. 45.97000122 -126.84002686]

Translation:

[[ -1.18324408 -58.9149482 135.93672542]]

Concatenate transformations: curve --> straight --> affine...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_curve2straightAffine.nii.gz -R template.nii straight2templateAffine.txt warp_curve2straight.nii.gz # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

Apply transformation...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/data_1mm_rpi.nii -o /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/data_1mm_rpi_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n 'BSpline[3]' # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop.nii.gz -o /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Parse list of warping fields...

Get dimensions of data...

51 x 256 x 256 x 1

Apply transformation...

Apply transformation and resample to destination space...

/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/i

Saved diffs

Original text

Open file

##[debug]Evaluating condition for step: 'Run batch_processing.sh'
##[debug]Evaluating: success()
##[debug]Evaluating success:
##[debug]=> true
##[debug]Result: true
##[debug]Starting: Run batch_processing.sh
##[debug]Loading inputs
##[debug]Loading env
Run bash batch_processing.sh
##[debug]Overwrite 'shell' base on job defaults.
##[debug]/usr/bin/bash --noprofile --norc -e -o pipefail /home/runner/work/_temp/f60e562d-3117-4569-b195-998c6fbd3e40.sh

# For full verbose, uncomment the next line
# set -x

# Fetch OS type
if uname -a | grep -i  darwin > /dev/null 2>&1; then
  # OSX
  open_command="open"
elif uname -a | grep -i  linux > /dev/null 2>&1; then
  # Linux
  open_command="xdg-open"
fi

# Check if users wants to use his own data
if [[ -z "$SCT_BP_DOWNLOAD" ]]; then
	SCT_BP_DOWNLOAD=1
fi

# QC folder
if [[ -z "$SCT_BP_QC_FOLDER" ]]; then
	SCT_BP_QC_FOLDER=`pwd`/"qc_example_data"
fi

# Remove QC folder
if [ -z "$SCT_BP_NO_REMOVE_QC" -a -d "$SCT_BP_QC_FOLDER" ]; then
  echo "Removing $SCT_BP_QC_FOLDER folder."
  rm -rf "$SCT_BP_QC_FOLDER"
fi

# get starting time:
start=`date +%s`

# download example data
if [[ "$SCT_BP_DOWNLOAD" == "1" ]]; then
  sct_download_data -d sct_example_data
fi

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_download_data -d sct_example_data
--

Trying URL: https://github.com/spinalcordtoolbox/sct_example_data/releases/download/r20180525/20180525_sct_example_data.zip
Downloading: 20180525_sct_example_data.zip
Creating temporary folder (/tmp/sct-20220920171305.527191-2x2t1fb1)
Unzip data to: /tmp/sct-20220920171305.527191-2x2t1fb1
Copying data to: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data
Removing temporary folders...
Done!

cd data/sct_example_data


# t2
# ===========================================================================================
cd t2
# Segment spinal cord
sct_deepseg_sc -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_deepseg_sc -i t2.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t2
  Threshold: 0.7
Creating temporary folder (/tmp/sct-20220920171307.373406-pm6k_6pk)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220920171318.141827-cb7xmz7v)
Remove temporary files...
rm -rf /tmp/sct-20220920171318.141827-cb7xmz7v
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Removing small objects above slice #240
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /tmp/sct-20220920171307.373406-pm6k_6pk

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_deepseg_sc/2022_09_20_171335.519968/bkg_img.png
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/style.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/main.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/animation.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/yaml.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/filesaver.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/f-icon.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyright.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keydown.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyup.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171335.519968.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars

  for dir in range(input.ndim)]
To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Tips: If you are not satisfied with the results you can try with another algorithm:
# sct_propseg -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"
# Vertebral labeling
# Tips: for manual initialization of labeling by clicking at disc C2-C3, use flag -initc2
sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Creating temporary folder (/tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx)

Copying input data to tmp folder...

Straighten spinal cord...
Creating temporary folder (/tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3)
Copy files to tmp folder...
Fitting centerline using B-spline approximation
Error on approximation = 1.45 mm
Error on approximation = 0.8 mm
Error on approximation = 0.78 mm
Error on approximation = 0.26 mm
Error on approximation = 0.18 mm
Error on approximation = 0.17 mm
Error on approximation = 0.19 mm
Error on approximation = 0.19 mm
Error on approximation = 0.19 mm
Create the straight space and the safe zone
Length of spinal cord: 195.1824594930412
Size of spinal cord in z direction: 191.2181565315654
Ratio length/size: 1.0207318333854003
Safe zone boundaries (curved space): [-122.38013064855659, 68.83802588300883]
Safe zone boundaries (straight space): [-124.36228212929447, 70.82017736374672]
Pad input volume to account for spinal cord length...
Time to generate centerline: 22.0 ms
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3
Generate output files...
mv /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
File created: ./data_straight.nii
Remove temporary files...
rm -rf /tmp/sct-20220920171338.432852-straighten_spinalcord-0de8cyy3

Resample to 0.5mm isotropic...
load data...

Apply straightening to segmentation...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -o segmentation_straight.nii -t warp_curve2straight.nii.gz -r data_straightr.nii -n Linear # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx
File /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/segmentation_straight.nii already exists. Will overwrite it.

Create label to identify disc...
Creating temporary folder...
Creating temporary folder (/tmp/sct-20220920171418.335766-17xtra4m)
Run C2-C3 detector...
C2-C3 detected...
Remove temporary files...
rm -rf /tmp/sct-20220920171418.335766-17xtra4m
File /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/labelz.nii.gz already exists. Will overwrite it.

And apply straightening to label...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -o labelz_straight.nii.gz -t warp_curve2straight.nii.gz -r data_straightr.nii -n NearestNeighbor # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

Get z and disc values from straight label...
.. [308, 3]
Look for template...
Path template: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
Open template and vertebral levels...
Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
Z-values for each disc: [963, 938, 907, 870, 833, 800, 769, 735, 692, 646, 600, 551, 500, 449, 396, 342, 289, 231, 168, 104, 79]
Distances between discs (in voxel): [25.0, 31.0, 37.0, 37.0, 33.0, 31.0, 34.0, 43.0, 46.0, 46.0, 49.0, 51.0, 51.0, 53.0, 54.0, 53.0, 58.0, 63.0, 64.0, 25.0]
Detect intervertebral discs...
Current disc: 2 (z=308). Direction: superior
.. Peak found: z=-2 (correlation = 0.5785475132964076)
Current disc: 1 (z=337). Direction: superior
.. correcting factor: 1.0
.. Switching to inferior direction.
Current disc: 3 (z=271). Direction: inferior
.. Peak found: z=-2 (correlation = 0.46669793555686756)
.. correcting factor: 1.0
Current disc: 4 (z=232). Direction: inferior
.. Peak found: z=0 (correlation = 0.4759131092619541)
.. correcting factor: 1.0
Current disc: 5 (z=199). Direction: inferior
.. Peak found: z=1 (correlation = 0.5489915159060484)
.. correcting factor: 0.9924242424242424
Current disc: 6 (z=169). Direction: inferior
.. Peak found: z=-1 (correlation = 0.6413729873029947)
.. correcting factor: 1.0003910068426198
Current disc: 7 (z=134). Direction: inferior
.. Peak found: z=3 (correlation = 0.49551596833735867)
.. correcting factor: 0.9856199566825753
Current disc: 8 (z=95). Direction: inferior
.. Peak found: z=2 (correlation = 0.5102032109234909)
.. correcting factor: 0.9777074711764266
Current disc: 9 (z=52). Direction: inferior
.. Peak found: z=2 (correlation = 0.5204922661088763)
.. correcting factor: 0.9723418633663299
Current disc: 10 (z=9). Direction: inferior
.. Peak found: z=6 (correlation = 0.5201107394731823)
.. correcting factor: 0.9585067770985733
Adding top disc based on adjusted template distance: #0
.. approximate distance: 24

Un-straighten labeling...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -o segmentation_labeled.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

Cleaning labeled segmentation:
  removing labeled voxels outside segmentation...
Done cleaning.
File /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/segmentation_labeled.nii already exists. Will overwrite it.

Label discs...

Un-straighten labeled discs...

Parse list of warping fields...

Get dimensions of data...
  101 x 139 x 392 x 1

Apply transformation...

Dilate labels before warping...
Creating temporary folder (/tmp/sct-20220920171426.359163-apply_transfo-6bexaavh)

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920171426.359163-apply_transfo-6bexaavh/dilated_data.nii -o segmentation_labeled_disc.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx
Copy affine matrix from destination space to make sure qform/sform are the same.

Take the center of mass of each registered dilated labels...
File segmentation_labeled_disc.nii already exists. Will overwrite it.

Remove temporary files...
rm -rf /tmp/sct-20220920171426.359163-apply_transfo-6bexaavh

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_seg_labeled.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_seg_labeled_discs.nii.gz
mv /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/warp_curve2straight.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_curve2straight.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_curve2straight.nii.gz
mv /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/warp_straight2curve.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_straight2curve.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_straight2curve.nii.gz
mv /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx/straight_ref.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/straight_ref.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/straight_ref.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920171338.139462-label_vertebrae-dgc0b1qx

*** Generate Quality Control (QC) html report ***
Resample images to NonexNone mm
QcImage: layout with Sagittal slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_label_vertebrae/2022_09_20_171431.921075/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171431.921075.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/math.py:113: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0. Please use `footprint` instead.

  return dilation(data, selem=_get_selem(shape, size, dim), out=None)
To see the results in a browser, type:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/math.py:113: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0. Please use `footprint` instead.
  return dilation(data, selem=_get_selem(shape, size, dim), out=None)
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Create labels at in the cord at C2 and C5 mid-vertebral levels
sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 2,5 -o labels_vert.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 2,5 -o labels_vert.nii.gz
--

Generating output files...
# Tips: you can also create labels manually using:
# sct_label_utils -i t2.nii.gz -create-viewer 2,5 -o labels_vert.nii.gz
# Register to template
sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels_vert.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels_vert.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Check template files...
  OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz
  OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz
  OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz

Check parameters:
  Data:                 t2.nii.gz
  Landmarks:            labels_vert.nii.gz
  Segmentation:         t2_seg.nii.gz
  Path template:        /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Remove temp files:    1

Check input labels...
Creating temporary folder (/tmp/sct-20220920171437.034485-register_to_template-gbfw5k06)

Copying input data to tmp folder and convert to nii...

Generate labels from template vertebral labeling

Check if provided labels are available in the template

Binarize segmentation

Resample data to 1mm isotropic...
load data...
load data...
To avoid intensity overflow due to convertion to +uint8+, intensity will be rescaled to the maximum quantization scale

Change orientation of input images to RPI...

Straighten the spinal cord using centerline/segmentation...
Creating temporary folder (/tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps)
Copy files to tmp folder...
Create the straight space and the safe zone
Length of spinal cord: 194.86777391248705
Size of spinal cord in z direction: 191.01429026627324
Ratio length/size: 1.0201737976820586
Safe zone boundaries (curved space): [-122.3822868551715, 68.63200341110175]
Safe zone boundaries (straight space): [-124.3090286782784, 70.55874523420866]
Pad input volume to account for spinal cord length...
Time to generate centerline: 18.0 ms
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps
Generate output files...
mv /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
mv /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps/tmp.anat_rigid_warp.nii.gz /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop_straight.nii.gz
File created: /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop_straight.nii.gz
Remove temporary files...
rm -rf /tmp/sct-20220920171442.832612-straighten_spinalcord-17dt4wps
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

Remove unused label on template. Keep only label present in the input label image...
File template_label_body.nii.gz already exists. Will overwrite it.

Dilating input labels using 3vox ball radius

Apply straightening to labels...

Parse list of warping fields...

Get dimensions of data...
  51 x 256 x 256 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/label_projected_1mm_rpi_dilate.nii.gz -o /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/label_projected_1mm_rpi_dilate_straight.nii.gz -t warp_curve2straight.nii.gz -r /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06
Copy affine matrix from destination space to make sure qform/sform are the same.

Estimate transformation for step #0...
Labels src: [[-0.49785977044107455, -12.840075485893843, 35.579769644543646], [-1.868628377073808, -13.049818470161009, -17.3863725163054]]
Labels dest: [[-0.0, 46.220001220703125, -100.34002685546875], [-0.0, 45.720001220703125, -153.34002685546875]]
Degrees of freedom (dof): Tx_Ty_Tz_Sz
Optimization terminated successfully.
         Current function value: 0.981628
         Iterations: 2
         Function evaluations: 151
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [   0.           45.97000122 -126.84002686]
Translation:
 [[ -1.18324408 -58.9149482  135.93672542]]

Concatenate transformations: curve --> straight --> affine...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_curve2straightAffine.nii.gz -R template.nii straight2templateAffine.txt warp_curve2straight.nii.gz # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

Apply transformation...

Parse list of warping fields...

Get dimensions of data...
  51 x 256 x 256 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/data_1mm_rpi.nii -o /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/data_1mm_rpi_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n 'BSpline[3]' # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06
Copy affine matrix from destination space to make sure qform/sform are the same.

Parse list of warping fields...

Get dimensions of data...
  51 x 256 x 193 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop.nii.gz -o /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/seg_bin_1mm_rpi_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06
Copy affine matrix from destination space to make sure qform/sform are the same.

Crop data in template space (for faster processing)...

Sub-sample in z-direction (for faster processing)...
load data...
load data...
load data...
load data...

Register straight spinal cord to template...
Creating temporary folder (/tmp/sct-20220920171531.753703-register-j00rwkzv)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #1
Registration parameters:
  type ........... imseg
  algo ........... centermassrot
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pcahog
Creating temporary folder (/tmp/sct-20220920171531.972062-register-lg1keqn0)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 141 x 141 x 97
  voxel size: 0.5mm x 0.5mm x 97mm

Split input segmentation...

Split destination segmentation...

Split input image...

Split destination image...
Switched to method 'hog' for slice: 0
Switched to method 'hog' for slice: 8
Switched to method 'hog' for slice: 14
Switched to method 'hog' for slice: 15
Switched to method 'hog' for slice: 92
Switched to method 'hog' for slice: 93
Switched to method 'hog' for slice: 94
Switched to method 'hog' for slice: 94
Switched to method 'hog' for slice: 95
Switched to method 'hog' for slice: 95
Switched to method 'hog' for slice: 96
Switched to method 'hog' for slice: 96

Generate warping field...
 --> step1Warp.nii.gz

Generate warping field...
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220920171531.753703-register-j00rwkzv
cp step1InverseWarp.nii.gz /tmp/sct-20220920171531.753703-register-j00rwkzv
rm -rf /tmp/sct-20220920171531.972062-register-lg1keqn0

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 97 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920171531.753703-register-j00rwkzv
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 1
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Generate output files...

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 1mm --restrict-deformation 1x1x0 --output '[step2,src_seg_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171531.753703-register-j00rwkzv

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz # in /tmp/sct-20220920171531.753703-register-j00rwkzv
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220920171531.753703-register-j00rwkzv

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 97 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220920171531.753703-register-j00rwkzv
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 97 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220920171531.753703-register-j00rwkzv
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
mv /tmp/sct-20220920171531.753703-register-j00rwkzv/src_reg.nii data_1mm_rpi_straightAffine_crop_sub_reg.nii
File created: data_1mm_rpi_straightAffine_crop_sub_reg.nii
mv /tmp/sct-20220920171531.753703-register-j00rwkzv/warp_src2dest.nii.gz warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz
File created: warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz
mv /tmp/sct-20220920171531.753703-register-j00rwkzv/dest_reg.nii template_crop_sub_reg.nii
File created: template_crop_sub_reg.nii
mv /tmp/sct-20220920171531.753703-register-j00rwkzv/warp_dest2src.nii.gz warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz
File created: warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920171531.753703-register-j00rwkzv

Concatenate transformations: anat --> template...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_anat2template.nii.gz -R template.nii warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz warp_curve2straightAffine.nii.gz # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

Concatenate transformations: template --> anat...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_template2anat.nii.gz -R data.nii warp_straight2curve.nii.gz -i straight2templateAffine.txt warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i template.nii -o template2anat.nii.gz -t warp_template2anat.nii.gz -r data.nii -n 'BSpline[3]' # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06
Copy affine matrix from destination space to make sure qform/sform are the same.

Parse list of warping fields...

Get dimensions of data...
  64 x 320 x 320 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o anat2template.nii.gz -t warp_anat2template.nii.gz -r template.nii -n 'BSpline[3]' # in /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
mv /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/warp_template2anat.nii.gz warp_template2anat.nii.gz
File created: warp_template2anat.nii.gz
mv /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/warp_anat2template.nii.gz warp_anat2template.nii.gz
File created: warp_anat2template.nii.gz
mv /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/template2anat.nii.gz template2anat.nii.gz
File created: template2anat.nii.gz
mv /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/anat2template.nii.gz anat2template.nii.gz
File created: anat2template.nii.gz
File warp_curve2straight.nii.gz already exists. Deleting it..
mv /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
File created: warp_curve2straight.nii.gz
File warp_straight2curve.nii.gz already exists. Deleting it..
mv /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
File created: warp_straight2curve.nii.gz
File straight_ref.nii.gz already exists. Deleting it..
mv /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06/straight_ref.nii.gz straight_ref.nii.gz
File created: straight_ref.nii.gz

Delete temporary files...
rm -rf /tmp/sct-20220920171437.034485-register_to_template-gbfw5k06

Finished! Elapsed time: 200s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_register_to_template/2022_09_20_171803.417566/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171803.417566.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/math.py:113: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0. Please use `footprint` instead.

  return dilation(data, selem=_get_selem(shape, size, dim), out=None)
To see the results in a browser, type:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars
  for dir in range(input.ndim)]
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Tips: If you are not satisfied with the results, you can tweak registration parameters.
# For example here, we would like to take into account the rotation of the cord, as well as
# adding a 3rd registration step that uses the image intensity (not only cord segmentations).
# so we could do something like this:
# sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2s.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d t2s.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=seg,algo=slicereg,smooth=3:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz
# Warp template without the white matter atlas (we don't need it at this point)
sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
  Destination image ........ t2.nii.gz
  Warping field ............ warp_template2anat.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template
# Compute cross-sectional area (and other morphometry measures) for each slice
sct_process_segmentation -i t2_seg.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_process_segmentation -i t2_seg.nii.gz
--


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/csa.csv

# Compute cross-sectional area and average between C2 and C3 levels
sct_process_segmentation -i t2_seg.nii.gz -vert 2:3 -o csa_c2c3.csv

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_process_segmentation -i t2_seg.nii.gz -vert 2:3 -o csa_c2c3.csv
--


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/csa_c2c3.csv

# Compute cross-sectionnal area based on distance from pontomedullary junction (PMJ)
# Detect PMJ
sct_detect_pmj -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER" 

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_detect_pmj -i t2.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Creating temporary folder (/tmp/sct-20220920171858.460730-heyivh1k)
cp t2.nii.gz /tmp/sct-20220920171858.460730-heyivh1k
Bounding box: x=[0, 320], y=[0, 320], z=[32, 34]
Cropping the image...

Run PMJ detector
['isct_spine_detect', '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models/t2_model', 't2_midSag', 't2_map_pmj']

Ponto-Medullary Junction detected
.. Peak found: x=-4 (correlation = 0.5729094434043677)
R-L coordinate adjusted from 32 to  28)
Bounding box: x=[0, 320], y=[0, 320], z=[28, 30]
Cropping the image...
File t2_midSag.nii already exists. Will overwrite it.

Run PMJ detector
['isct_spine_detect', '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models/t2_model', 't2_midSag', 't2_map_pmj.nii']

Ponto-Medullary Junction detected
	x_pmj = 35
	y_pmj = 151
	z_pmj = 259

Save resulting file...
cp /tmp/sct-20220920171858.460730-heyivh1k/t2_pmj.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_pmj.nii.gz
rm -rf /tmp/sct-20220920171858.460730-heyivh1k

*** Generate Quality Control (QC) html report ***
Resample images to NonexNone mm
QcImage: layout with Sagittal slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_detect_pmj/2022_09_20_171901.431748/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171901.431748.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute cross-section area at 60 mm from PMJ averaged on a 30 mm extent
sct_process_segmentation -i t2_seg.nii.gz -pmj t2_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -qc "$SCT_BP_QC_FOLDER" -qc-image t2.nii.gz -o csa_pmj.csv

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_process_segmentation -i t2_seg.nii.gz -pmj t2_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data -qc-image t2.nii.gz -o csa_pmj.csv
--

Creating temporary folder (/tmp/sct-20220920171905.954467-uhz63tss)

*** Generate Quality Control (QC) html report ***
Resample images to NonexNone mm
QcImage: layout with Sagittal slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_process_segmentation/2022_09_20_171907.261164/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171907.261164.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/csa_pmj.csv

# Go back to root folder
cd ..


# t2s (stands for t2-star)
# ===========================================================================================
cd t2s
# Spinal cord segmentation
sct_deepseg_sc -i t2s.nii.gz -c t2s -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_deepseg_sc -i t2s.nii.gz -c t2s -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: False
  Kernel dimension: 2d
  Contrast: t2s
  Threshold: 0.89
Creating temporary folder (/tmp/sct-20220920171909.753942-wep22vdi)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220920171910.773644-0a_efzoz)
Remove temporary files...
rm -rf /tmp/sct-20220920171910.773644-0a_efzoz
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Removing small objects above slice #30
Remove temporary files...
rm -rf /tmp/sct-20220920171909.753942-wep22vdi

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2s/sct_deepseg_sc/2022_09_20_171913.908718/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171913.908718.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

  for dir in range(input.ndim)]
# Segment gray matter
sct_deepseg_gm -i t2s.nii.gz -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_deepseg_gm -i t2s.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2s/sct_deepseg_gm/2022_09_20_171932.390122/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_171932.390122.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars

  for dir in range(input.ndim)]
To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register template->t2s (using warping field generated from template<->t2 registration)
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2s.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d t2s.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,algo=syn,slicewise=1,iter=1,metric=CC -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2s.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d t2s.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,algo=syn,slicewise=1,iter=1,metric=CC -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t2s.nii.gz
  Destination ......... t2s.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920171935.370710-register-52m_yyk_)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920171935.370710-register-52m_yyk_
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... centermass
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220920171938.092576-register-sdr8orgz)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 320 x 320 x 32
  voxel size: 0.5mm x 0.5mm x 32mm

Split input segmentation...

Split destination segmentation...
Slice #0 is empty. It will be ignored.
Slice #1 is empty. It will be ignored.
Slice #31 is empty. It will be ignored.

Generate warping field...
 --> step1Warp.nii.gz

Generate warping field...
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220920171935.370710-register-52m_yyk_
cp step1InverseWarp.nii.gz /tmp/sct-20220920171935.370710-register-52m_yyk_
rm -rf /tmp/sct-20220920171938.092576-register-sdr8orgz

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920171935.370710-register-52m_yyk_
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 1
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220920171950.841353-register-kp2nvw4i)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 320 x 320 x 32
  voxel size: 0.5mm x 0.5mm x 32mm

Split input volume...

Split destination volume...
Registering slice 0/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 1/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 2/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 3/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 4/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 5/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 6/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 7/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 8/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 9/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 10/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 11/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 12/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 13/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 14/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 15/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 16/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 17/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 18/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 19/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 20/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 21/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 22/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0022.nii,src_Z0022.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0022,src_Z0022_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 23/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0023.nii,src_Z0023.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0023,src_Z0023_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 24/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0024.nii,src_Z0024.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0024,src_Z0024_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 25/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0025.nii,src_Z0025.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0025,src_Z0025_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 26/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0026.nii,src_Z0026.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0026,src_Z0026_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 27/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0027.nii,src_Z0027.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0027,src_Z0027_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 28/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0028.nii,src_Z0028.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0028,src_Z0028_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 29/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0029.nii,src_Z0029.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0029,src_Z0029_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 30/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0030.nii,src_Z0030.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0030,src_Z0030_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i
Registering slice 31/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0031.nii,src_Z0031.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0031,src_Z0031_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920171950.841353-register-kp2nvw4i

Merge warping fields along z...

Move warping fields...
cp step2Warp.nii.gz /tmp/sct-20220920171935.370710-register-52m_yyk_
cp step2InverseWarp.nii.gz /tmp/sct-20220920171935.370710-register-52m_yyk_
rm -rf /tmp/sct-20220920171950.841353-register-kp2nvw4i

--
ESTIMATE TRANSFORMATION FOR STEP #3

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220920171935.370710-register-52m_yyk_
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 1
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220920172044.114446-register-yfcq9ju2)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 320 x 320 x 32
  voxel size: 0.5mm x 0.5mm x 32mm

Split input volume...

Split destination volume...
Registering slice 0/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 1/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 2/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 3/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 4/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 5/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 6/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 7/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 8/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 9/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 10/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 11/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 12/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 13/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 14/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 15/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 16/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 17/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 18/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 19/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 20/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 21/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 22/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0022.nii,src_Z0022.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0022,src_Z0022_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 23/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0023.nii,src_Z0023.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0023,src_Z0023_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 24/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0024.nii,src_Z0024.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0024,src_Z0024_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 25/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0025.nii,src_Z0025.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0025,src_Z0025_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 26/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0026.nii,src_Z0026.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0026,src_Z0026_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 27/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0027.nii,src_Z0027.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0027,src_Z0027_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 28/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0028.nii,src_Z0028.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0028,src_Z0028_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 29/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0029.nii,src_Z0029.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0029,src_Z0029_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 30/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0030.nii,src_Z0030.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0030,src_Z0030_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2
Registering slice 31/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0031.nii,src_Z0031.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0031,src_Z0031_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172044.114446-register-yfcq9ju2

Merge warping fields along z...

Move warping fields...
cp step3Warp.nii.gz /tmp/sct-20220920171935.370710-register-52m_yyk_
cp step3InverseWarp.nii.gz /tmp/sct-20220920171935.370710-register-52m_yyk_
rm -rf /tmp/sct-20220920172044.114446-register-yfcq9ju2

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_3.nii.gz warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220920171935.370710-register-52m_yyk_
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz warp_inverse_3.nii.gz # in /tmp/sct-20220920171935.370710-register-52m_yyk_

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220920171935.370710-register-52m_yyk_
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  320 x 320 x 32 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220920171935.370710-register-52m_yyk_
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: PAM50_t2s_reg.nii.gz
mv /tmp/sct-20220920171935.370710-register-52m_yyk_/warp_src2dest.nii.gz warp_template2t2s.nii.gz
File created: warp_template2t2s.nii.gz
File created: t2s_reg.nii.gz
mv /tmp/sct-20220920171935.370710-register-52m_yyk_/warp_dest2src.nii.gz warp_t2s2template.nii.gz
File created: warp_t2s2template.nii.gz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/registration/algorithms.py:1443: RuntimeWarning: Mean of empty slice.

  centermass = coordsrc.mean(0)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:182: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:263: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims, where=where)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in true_divide
  subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/registration/algorithms.py:1443: RuntimeWarning: Mean of empty slice.
  centermass = coordsrc.mean(0)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:182: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:263: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims, where=where)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in true_divide
  subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/registration/algorithms.py:1443: RuntimeWarning: Mean of empty slice.
  centermass = coordsrc.mean(0)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:182: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:263: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims, where=where)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in true_divide
  subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
Remove temporary files...
rm -rf /tmp/sct-20220920171935.370710-register-52m_yyk_

Finished! Elapsed time: 107s
# Warp template
sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
  Destination image ........ t2s.nii.gz
  Warping field ............ warp_template2t2s.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas
# Subtract GM segmentation from cord segmentation to obtain WM segmentation
sct_maths -i t2s_seg.nii.gz -sub t2s_gmseg.nii.gz -o t2s_wmseg.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_maths -i t2s_seg.nii.gz -sub t2s_gmseg.nii.gz -o t2s_wmseg.nii.gz
--

# Compute cross-sectional area of the gray and white matter between C2 and C5
sct_process_segmentation -i t2s_wmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_wm.csv

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_process_segmentation -i t2s_wmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_wm.csv
--


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s/csa_wm.csv

sct_process_segmentation -i t2s_gmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_gm.csv

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_process_segmentation -i t2s_gmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_gm.csv
--


No properties for slice: 3

Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s/csa_gm.csv

# OPTIONAL: Update template registration using information from gray matter segmentation
# # <<<
# # Register WM/GM template to WM/GM seg
# sct_register_multimodal -i ../../../data/PAM50/template/PAM50_wm.nii.gz -d t2s_wmseg.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=im,algo=syn,slicewise=1,iter=5 -initwarp warp_template2t2s.nii.gz -initwarpinv warp_t2s2template.nii.gz -qc "$SCT_BP_QC_FOLDER" -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz
# # Warp template (this time corrected for internal structure)
# sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz
# # >>>
cd ..


# t1
# ===========================================================================================
cd t1
# Contrast-agnostic registration
# 1. t1w preprocessing (cropping around spinal cord)
sct_deepseg_sc -i t1.nii.gz -c t1 -centerline cnn

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_deepseg_sc -i t1.nii.gz -c t1 -centerline cnn
--

Config deepseg_sc:
  Centerline algorithm: cnn
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t1
  Threshold: 0.15
Creating temporary folder (/tmp/sct-20220920172305.924919-urrupr_s)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
To avoid intensity overflow due to convertion to +uint8+, intensity will be rescaled to the maximum quantization scale
Brain section detected.
Creating temporary folder (/tmp/sct-20220920172334.661231-45s3kzqr)
Remove temporary files...
rm -rf /tmp/sct-20220920172334.661231-45s3kzqr
Cropping brain section.
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /tmp/sct-20220920172305.924919-urrupr_s
sct_create_mask -i t1.nii.gz -p centerline,t1_seg.nii.gz -size 35mm -f cylinder -o mask_t1.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_create_mask -i t1.nii.gz -p centerline,t1_seg.nii.gz -size 35mm -f cylinder -o mask_t1.nii.gz
--

  OK: t1_seg.nii.gz
Creating temporary folder (/tmp/sct-20220920172358.659809-create_mask-sam7yra6)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:228: DeprecationWarning: get_header method is deprecated.

Please use the ``img.header`` property instead.
Orientation:

  LPI
* deprecated from version: 2.1

* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
Dimensions:
  hdr = centerline.get_header()  # get header
(192, 260, 320, 1, 0.9999965, 1.0, 1.0, 1)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:231: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).


Create mask...
* deprecated from version: 3.0

* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
Remove temporary files...
  data_centerline = centerline.get_data()  # get centerline
rm -rf /tmp/sct-20220920172358.659809-create_mask-sam7yra6
sct_crop_image -i t1.nii.gz -m mask_t1.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_crop_image -i t1.nii.gz -m mask_t1.nii.gz
--

Bounding box: x=[72, 114], y=[57, 124], z=[0, 174]
Cropping the image...
# 2. t2w preprocessing (cropping around spinal cord)
cp ../t2/t2.nii.gz ./t2.nii.gz
sct_deepseg_sc -i t2.nii.gz -c t2

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_deepseg_sc -i t2.nii.gz -c t2
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t2
  Threshold: 0.7
Creating temporary folder (/tmp/sct-20220920172403.708349-dzfynh6d)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220920172413.401876-i8u3ng3_)
Remove temporary files...
rm -rf /tmp/sct-20220920172413.401876-i8u3ng3_
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Removing small objects above slice #240
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /tmp/sct-20220920172403.708349-dzfynh6d
sct_create_mask -i t2.nii.gz -p centerline,t2_seg.nii.gz -size 35mm -f cylinder -o mask_t2.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_create_mask -i t2.nii.gz -p centerline,t2_seg.nii.gz -size 35mm -f cylinder -o mask_t2.nii.gz
--

  OK: t2_seg.nii.gz
Creating temporary folder (/tmp/sct-20220920172428.638090-create_mask-2s5r_a5f)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:228: DeprecationWarning: get_header method is deprecated.

Please use the ``img.header`` property instead.
Orientation:

  LPI
* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:231: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline

Dimensions:
(64, 320, 320, 1, 0.8000004, 0.8, 0.8, 1)

Create mask...

Remove temporary files...
rm -rf /tmp/sct-20220920172428.638090-create_mask-2s5r_a5f
sct_crop_image -i t2.nii.gz -m mask_t2.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_crop_image -i t2.nii.gz -m mask_t2.nii.gz
--

Bounding box: x=[8, 56], y=[71, 161], z=[0, 240]
Cropping the image...
# 3. Perform registration
sct_register_multimodal -i t1_crop.nii.gz -d t2_crop.nii.gz -param step=1,type=im,algo=dl

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i t1_crop.nii.gz -d t2_crop.nii.gz -param step=1,type=im,algo=dl
--


Input parameters:
  Source .............. t1_crop.nii.gz
  Destination ......... t2_crop.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920172432.998861-register-s5jd265e)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172432.998861-register-s5jd265e

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  42 x 67 x 174 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220920172432.998861-register-s5jd265e
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... im
  algo ........... dl
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Preprocess data by setting an isotropic resolution of 1mm and bringing the source image into same space as moving image...
load data...
Creating temporary folder (/tmp/sct-20220920172434.781820-register-dfxwuyo2)

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct-20220920172434.781820-register-dfxwuyo2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct-20220920172434.781820-register-dfxwuyo2

Parse list of warping fields...

Get dimensions of data...
  48 x 90 x 240 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220920172434.781820-register-dfxwuyo2
Copy affine matrix from destination space to make sure qform/sform are the same.

Parse list of warping fields...

Get dimensions of data...
  38 x 72 x 192 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220920172434.781820-register-dfxwuyo2
Copy affine matrix from destination space to make sure qform/sform are the same.
mv /tmp/sct-20220920172434.781820-register-dfxwuyo2/src_reg.nii src_reg_same_space.nii
File created: src_reg_same_space.nii
mv /tmp/sct-20220920172434.781820-register-dfxwuyo2/warp_src2dest.nii.gz warp_src_reg2dest_RPI_iso_res.nii.gz
File created: warp_src_reg2dest_RPI_iso_res.nii.gz
mv /tmp/sct-20220920172434.781820-register-dfxwuyo2/dest_reg.nii src_reg_same_space_inv.nii
File created: src_reg_same_space_inv.nii
mv /tmp/sct-20220920172434.781820-register-dfxwuyo2/warp_dest2src.nii.gz warp_dest_RPI_iso_res2src_reg.nii.gz
File created: warp_dest_RPI_iso_res2src_reg.nii.gz

Load data to register...

 Creating data tensors...

 Input shape for fixed tensor: torch.Size([1, 1, 48, 80, 192])

 Input shape for moving tensor: torch.Size([1, 1, 48, 80, 192])

 Creating VxmDense models with arguments:

{'inshape': [48, 80, 192], 'int_steps': 5, 'int_downsize': 2, 'unet_half_res': True, 'nb_unet_features': ([256, 256, 256, 256], [256, 256, 256, 256, 256, 256])}

 Loading first VxmDense model...

 Loading second VxmDense model...

 Predicting using first VxmDense model...

 Predicting using second VxmDense model...

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20220920172432.998861-register-s5jd265e
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20220920172432.998861-register-s5jd265e

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  42 x 67 x 174 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220920172432.998861-register-s5jd265e
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  48 x 90 x 240 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220920172432.998861-register-s5jd265e
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: t1_crop_reg.nii.gz
mv /tmp/sct-20220920172432.998861-register-s5jd265e/warp_src2dest.nii.gz warp_t1_crop2t2_crop.nii.gz
File created: warp_t1_crop2t2_crop.nii.gz
File created: t2_crop_reg.nii.gz
mv /tmp/sct-20220920172432.998861-register-s5jd265e/warp_dest2src.nii.gz warp_t2_crop2t1_crop.nii.gz
File created: warp_t2_crop2t1_crop.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172432.998861-register-s5jd265e

Finished! Elapsed time: 28s

# Other useful utilities
# 1. Smooth spinal cord along superior-inferior axis
sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz
--


Check input arguments...
  Volume to smooth .................. t1.nii.gz
  Centerline ........................ t1_seg.nii.gz
  Sigma (mm) ........................ [0, 0, 3]
  Verbose ........................... 1
Creating temporary folder (/tmp/sct-20220920172507.407393-smooth_spinalcord-0a3m9imy)

Copying input data to tmp folder and convert to nii...
cp t1.nii.gz /tmp/sct-20220920172507.407393-smooth_spinalcord-0a3m9imy/anat.nii.gz
cp t1_seg.nii.gz /tmp/sct-20220920172507.407393-smooth_spinalcord-0a3m9imy/centerline.nii.gz

Orient input volume to RPI orientation...

Orient centerline to RPI orientation...

Straighten the spinal cord using centerline/segmentation...
Creating temporary folder (/tmp/sct-20220920172508.568375-straighten_spinalcord-qa8m9pqs)
Copy files to tmp folder...
Fitting centerline using B-spline approximation
Error on approximation = 0.4 mm
Error on approximation = 0.32 mm
Error on approximation = 0.26 mm
Error on approximation = 0.08 mm
Error on approximation = 0.08 mm
Error on approximation = 0.04 mm
Error on approximation = 0.03 mm
Error on approximation = 0.03 mm
Create the straight space and the safe zone
Length of spinal cord: 176.60968855611546
Size of spinal cord in z direction: 173.1710381900656
Ratio length/size: 1.019856959928113
Safe zone boundaries (curved space): [-107.36701470917797, 65.80402348088762]
Safe zone boundaries (straight space): [-109.0863398922029, 67.52334866391256]
Pad input volume to account for spinal cord length...
Time to generate centerline: 16.0 ms
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172508.568375-straighten_spinalcord-qa8m9pqs
Generate output files...
mv /tmp/sct-20220920172508.568375-straighten_spinalcord-qa8m9pqs/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /tmp/sct-20220920172508.568375-straighten_spinalcord-qa8m9pqs/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20220920172508.568375-straighten_spinalcord-qa8m9pqs/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
File created: ./anat_rpi_straight.nii
Remove temporary files...
rm -rf /tmp/sct-20220920172508.568375-straighten_spinalcord-qa8m9pqs

Finished! Elapsed time: 67 s
cp straight_ref.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t1/straight_ref.nii.gz
cp warp_curve2straight.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t1/warp_curve2straight.nii.gz
cp warp_straight2curve.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t1/warp_straight2curve.nii.gz

Smooth the straightened image...

Apply the reversed warping field to get back the curved spinal cord...

Parse list of warping fields...

Get dimensions of data...
  71 x 71 x 178 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i anat_rpi_straight_smooth.nii -o anat_rpi_straight_smooth_curved.nii -t warp_straight2curve.nii.gz -r anat.nii -n 'BSpline[3]' # in /tmp/sct-20220920172507.407393-smooth_spinalcord-0a3m9imy
Copy affine matrix from destination space to make sure qform/sform are the same.

Replace zeroed voxels by original image...

Generate output file...
File created: t1_smooth.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172507.407393-smooth_spinalcord-0a3m9imy

Finished! Elapsed time: 78s

# 2. Flatten cord in the right-left direction (to make nice figure)
sct_flatten_sagittal -i t1.nii.gz -s t1_seg.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_flatten_sagittal -i t1.nii.gz -s t1_seg.nii.gz
--

# Go back to root folder
cd ..


# mt
# ===========================================================================================
cd mt
# Get centerline from mt1 data
sct_get_centerline -i mt1.nii.gz -c t2

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_get_centerline -i mt1.nii.gz -c t2
--

Creating temporary folder (/tmp/sct-20220920172630.540915-9dnqunyb)
Remove temporary files...
rm -rf /tmp/sct-20220920172630.540915-9dnqunyb
# sct_get_centerline -i mt1.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"
# Create mask
sct_create_mask -i mt1.nii.gz -p centerline,mt1_centerline.nii.gz -size 45mm

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_create_mask -i mt1.nii.gz -p centerline,mt1_centerline.nii.gz -size 45mm
--

  OK: mt1_centerline.nii.gz
Creating temporary folder (/tmp/sct-20220920172632.342684-create_mask-vx8dfebq)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:228: DeprecationWarning: get_header method is deprecated.

Please use the ``img.header`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:231: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline
Orientation:
  LPI

Dimensions:
(192, 192, 22, 1, 0.8958333, 0.8958333, 5.000001, 1)

Create mask...

Remove temporary files...
rm -rf /tmp/sct-20220920172632.342684-create_mask-vx8dfebq
# Crop data for faster processing
sct_crop_image -i mt1.nii.gz -m mask_mt1.nii.gz -o mt1_crop.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_crop_image -i mt1.nii.gz -m mask_mt1.nii.gz -o mt1_crop.nii.gz
--

Bounding box: x=[64, 125], y=[62, 119], z=[0, 22]
Cropping the image...
# Segment spinal cord
sct_deepseg_sc -i mt1_crop.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_deepseg_sc -i mt1_crop.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t2
  Threshold: 0.7
Creating temporary folder (/tmp/sct-20220920172634.732193-2rj8vxgn)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220920172634.796362-bw74kgjr)
Remove temporary files...
rm -rf /tmp/sct-20220920172634.796362-bw74kgjr
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Remove temporary files...
rm -rf /tmp/sct-20220920172634.732193-2rj8vxgn

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_deepseg_sc/2022_09_20_172635.603645/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172635.603645.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register mt0->mt1
# Tips: here we only use rigid transformation because both images have very similar sequence parameters. We don't want to use SyN/BSplineSyN to avoid introducing spurious deformations.
# Tips: here we input -dseg because it is needed by the QC report
sct_register_multimodal -i mt0.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i mt0.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Input parameters:
  Source .............. mt0.nii.gz
  Destination ......... mt1_crop.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920172638.268469-register-uaicgh5f)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.268469-register-uaicgh5f

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  192 x 192 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220920172638.268469-register-uaicgh5f
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... im
  algo ........... rigid
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220920172638.682389-register-gq3bre3s)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 61 x 57 x 22
  voxel size: 0.8958333mm x 0.8958333mm x 22mm

Split input volume...

Split destination volume...
Registering slice 0/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0000.nii,src_Z0000.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000Warp.nii.gz -R dest_Z0000.nii warp2d_null0Warp.nii.gz warp2d_00000GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000InverseWarp.nii.gz -R src_Z0000.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00000GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 1/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0001.nii,src_Z0001.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010Warp.nii.gz -R dest_Z0001.nii warp2d_null0Warp.nii.gz warp2d_00010GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010InverseWarp.nii.gz -R src_Z0001.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00010GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 2/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0002.nii,src_Z0002.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020Warp.nii.gz -R dest_Z0002.nii warp2d_null0Warp.nii.gz warp2d_00020GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020InverseWarp.nii.gz -R src_Z0002.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00020GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 3/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0003.nii,src_Z0003.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030Warp.nii.gz -R dest_Z0003.nii warp2d_null0Warp.nii.gz warp2d_00030GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030InverseWarp.nii.gz -R src_Z0003.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00030GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 4/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0004.nii,src_Z0004.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040Warp.nii.gz -R dest_Z0004.nii warp2d_null0Warp.nii.gz warp2d_00040GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040InverseWarp.nii.gz -R src_Z0004.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00040GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 5/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0005.nii,src_Z0005.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050Warp.nii.gz -R dest_Z0005.nii warp2d_null0Warp.nii.gz warp2d_00050GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050InverseWarp.nii.gz -R src_Z0005.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00050GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 6/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0006.nii,src_Z0006.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060Warp.nii.gz -R dest_Z0006.nii warp2d_null0Warp.nii.gz warp2d_00060GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060InverseWarp.nii.gz -R src_Z0006.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00060GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 7/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0007.nii,src_Z0007.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070Warp.nii.gz -R dest_Z0007.nii warp2d_null0Warp.nii.gz warp2d_00070GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070InverseWarp.nii.gz -R src_Z0007.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00070GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 8/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0008.nii,src_Z0008.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080Warp.nii.gz -R dest_Z0008.nii warp2d_null0Warp.nii.gz warp2d_00080GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080InverseWarp.nii.gz -R src_Z0008.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00080GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 9/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0009.nii,src_Z0009.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090Warp.nii.gz -R dest_Z0009.nii warp2d_null0Warp.nii.gz warp2d_00090GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090InverseWarp.nii.gz -R src_Z0009.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00090GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 10/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0010.nii,src_Z0010.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100Warp.nii.gz -R dest_Z0010.nii warp2d_null0Warp.nii.gz warp2d_00100GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100InverseWarp.nii.gz -R src_Z0010.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00100GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 11/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0011.nii,src_Z0011.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110Warp.nii.gz -R dest_Z0011.nii warp2d_null0Warp.nii.gz warp2d_00110GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110InverseWarp.nii.gz -R src_Z0011.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00110GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 12/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0012.nii,src_Z0012.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120Warp.nii.gz -R dest_Z0012.nii warp2d_null0Warp.nii.gz warp2d_00120GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120InverseWarp.nii.gz -R src_Z0012.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00120GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 13/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0013.nii,src_Z0013.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130Warp.nii.gz -R dest_Z0013.nii warp2d_null0Warp.nii.gz warp2d_00130GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130InverseWarp.nii.gz -R src_Z0013.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00130GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 14/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0014.nii,src_Z0014.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140Warp.nii.gz -R dest_Z0014.nii warp2d_null0Warp.nii.gz warp2d_00140GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140InverseWarp.nii.gz -R src_Z0014.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00140GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 15/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0015.nii,src_Z0015.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150Warp.nii.gz -R dest_Z0015.nii warp2d_null0Warp.nii.gz warp2d_00150GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150InverseWarp.nii.gz -R src_Z0015.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00150GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 16/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0016.nii,src_Z0016.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160Warp.nii.gz -R dest_Z0016.nii warp2d_null0Warp.nii.gz warp2d_00160GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160InverseWarp.nii.gz -R src_Z0016.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00160GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 17/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0017.nii,src_Z0017.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170Warp.nii.gz -R dest_Z0017.nii warp2d_null0Warp.nii.gz warp2d_00170GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170InverseWarp.nii.gz -R src_Z0017.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00170GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 18/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0018.nii,src_Z0018.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180Warp.nii.gz -R dest_Z0018.nii warp2d_null0Warp.nii.gz warp2d_00180GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180InverseWarp.nii.gz -R src_Z0018.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00180GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 19/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0019.nii,src_Z0019.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190Warp.nii.gz -R dest_Z0019.nii warp2d_null0Warp.nii.gz warp2d_00190GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190InverseWarp.nii.gz -R src_Z0019.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00190GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 20/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0020.nii,src_Z0020.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200Warp.nii.gz -R dest_Z0020.nii warp2d_null0Warp.nii.gz warp2d_00200GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200InverseWarp.nii.gz -R src_Z0020.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00200GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
Registering slice 21/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0021.nii,src_Z0021.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210Warp.nii.gz -R dest_Z0021.nii warp2d_null0Warp.nii.gz warp2d_00210GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210InverseWarp.nii.gz -R src_Z0021.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00210GenericAffine.mat # in /tmp/sct-20220920172638.682389-register-gq3bre3s

Merge warping fields along z...

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220920172638.268469-register-uaicgh5f
cp step1InverseWarp.nii.gz /tmp/sct-20220920172638.268469-register-uaicgh5f
rm -rf /tmp/sct-20220920172638.682389-register-gq3bre3s

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20220920172638.268469-register-uaicgh5f
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20220920172638.268469-register-uaicgh5f

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  192 x 192 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n 'BSpline[3]' # in /tmp/sct-20220920172638.268469-register-uaicgh5f
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  61 x 57 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n 'BSpline[3]' # in /tmp/sct-20220920172638.268469-register-uaicgh5f
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: mt0_reg.nii.gz
mv /tmp/sct-20220920172638.268469-register-uaicgh5f/warp_src2dest.nii.gz warp_mt02mt1_crop.nii.gz
File created: warp_mt02mt1_crop.nii.gz
File created: mt1_crop_reg.nii.gz
mv /tmp/sct-20220920172638.268469-register-uaicgh5f/warp_dest2src.nii.gz warp_mt1_crop2mt0.nii.gz
File created: warp_mt1_crop2mt0.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172638.268469-register-uaicgh5f

Finished! Elapsed time: 10s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_register_multimodal/2022_09_20_172648.047126/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172648.047126.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register template->mt1
# Tips: here we only use the segmentations due to poor SC/CSF contrast at the bottom slice.
# Tips: First step: slicereg based on images, with large smoothing to capture potential motion between anat and mt, then at second step: bpslinesyn in order to adapt the shape of the cord to the mt modality (in case there are distortions between anat and mt).
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=seg,algo=slicereg,smooth=3:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2mt.nii.gz -owarpinv warp_mt2template.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=seg,algo=slicereg,smooth=3:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2mt.nii.gz -owarpinv warp_mt2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t2.nii.gz
  Destination ......... mt1_crop.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920172651.061999-register-hs730gw3)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920172651.061999-register-hs730gw3
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... slicereg
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 3
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsSliceRegularizedRegistration -t 'Translation[0.5]' -m 'MeanSquares[dest_seg_RPI_crop.nii,src_seg_reg_crop.nii,1,4,None,0.2]' -p 5 -i 10 -f 1 -s 3 -v 1 -o '[step1,src_seg_reg_crop_regStep1.nii]' # in /tmp/sct-20220920172651.061999-register-hs730gw3

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920172651.061999-register-hs730gw3
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 1
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220920172655.819159-register-szxsn47w)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 61 x 57 x 22
  voxel size: 0.8958333mm x 0.8958333mm x 22mm

Split input volume...

Split destination volume...
Registering slice 0/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 1/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 2/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 3/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 4/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 5/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 6/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 7/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 8/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 9/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 10/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 11/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 12/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 13/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 14/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 15/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 16/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 17/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 18/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 19/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 20/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w
Registering slice 21/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172655.819159-register-szxsn47w

Merge warping fields along z...

Move warping fields...
cp step2Warp.nii.gz /tmp/sct-20220920172651.061999-register-hs730gw3
cp step2InverseWarp.nii.gz /tmp/sct-20220920172651.061999-register-hs730gw3
rm -rf /tmp/sct-20220920172655.819159-register-szxsn47w

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220920172651.061999-register-hs730gw3
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220920172651.061999-register-hs730gw3

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220920172651.061999-register-hs730gw3
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  61 x 57 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220920172651.061999-register-hs730gw3
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: PAM50_t2_reg.nii.gz
mv /tmp/sct-20220920172651.061999-register-hs730gw3/warp_src2dest.nii.gz warp_template2mt.nii.gz
File created: warp_template2mt.nii.gz
File mt1_crop_reg.nii.gz already exists. Deleting it..
File created: mt1_crop_reg.nii.gz
mv /tmp/sct-20220920172651.061999-register-hs730gw3/warp_dest2src.nii.gz warp_mt2template.nii.gz
File created: warp_mt2template.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172651.061999-register-hs730gw3

Finished! Elapsed time: 22s
# Warp template
sct_warp_template -d mt1_crop.nii.gz -w warp_template2mt.nii.gz -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_warp_template -d mt1_crop.nii.gz -w warp_template2mt.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
  Destination image ........ mt1_crop.nii.gz
  Warping field ............ warp_template2mt.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_warp_template/2022_09_20_172746.348216/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172746.348216.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute mtr
sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1_crop.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1_crop.nii.gz
--


Compute MTR...
Found 0 voxels with value=0. These will be replaced by nan.
Threshold to clip values: +/- 100
# Register t1w->mt1
# Tips: We do not need to crop the t1w image before registration because step=0 of the registration is to put the source image in the space of the destination image (equivalent to cropping the t1w)
sct_register_multimodal -i t1w.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i t1w.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Input parameters:
  Source .............. t1w.nii.gz
  Destination ......... mt1_crop.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920172749.612429-register-qosxklja)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.612429-register-qosxklja

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  192 x 192 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220920172749.612429-register-qosxklja
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... im
  algo ........... rigid
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220920172749.989042-register-5c7xxd6y)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 61 x 57 x 22
  voxel size: 0.8958333mm x 0.8958333mm x 22mm

Split input volume...

Split destination volume...
Registering slice 0/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0000.nii,src_Z0000.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000Warp.nii.gz -R dest_Z0000.nii warp2d_null0Warp.nii.gz warp2d_00000GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000InverseWarp.nii.gz -R src_Z0000.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00000GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 1/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0001.nii,src_Z0001.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010Warp.nii.gz -R dest_Z0001.nii warp2d_null0Warp.nii.gz warp2d_00010GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010InverseWarp.nii.gz -R src_Z0001.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00010GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 2/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0002.nii,src_Z0002.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020Warp.nii.gz -R dest_Z0002.nii warp2d_null0Warp.nii.gz warp2d_00020GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020InverseWarp.nii.gz -R src_Z0002.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00020GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 3/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0003.nii,src_Z0003.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030Warp.nii.gz -R dest_Z0003.nii warp2d_null0Warp.nii.gz warp2d_00030GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030InverseWarp.nii.gz -R src_Z0003.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00030GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 4/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0004.nii,src_Z0004.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040Warp.nii.gz -R dest_Z0004.nii warp2d_null0Warp.nii.gz warp2d_00040GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040InverseWarp.nii.gz -R src_Z0004.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00040GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 5/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0005.nii,src_Z0005.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050Warp.nii.gz -R dest_Z0005.nii warp2d_null0Warp.nii.gz warp2d_00050GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050InverseWarp.nii.gz -R src_Z0005.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00050GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 6/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0006.nii,src_Z0006.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060Warp.nii.gz -R dest_Z0006.nii warp2d_null0Warp.nii.gz warp2d_00060GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060InverseWarp.nii.gz -R src_Z0006.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00060GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 7/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0007.nii,src_Z0007.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070Warp.nii.gz -R dest_Z0007.nii warp2d_null0Warp.nii.gz warp2d_00070GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070InverseWarp.nii.gz -R src_Z0007.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00070GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 8/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0008.nii,src_Z0008.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080Warp.nii.gz -R dest_Z0008.nii warp2d_null0Warp.nii.gz warp2d_00080GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080InverseWarp.nii.gz -R src_Z0008.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00080GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 9/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0009.nii,src_Z0009.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090Warp.nii.gz -R dest_Z0009.nii warp2d_null0Warp.nii.gz warp2d_00090GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090InverseWarp.nii.gz -R src_Z0009.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00090GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 10/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0010.nii,src_Z0010.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100Warp.nii.gz -R dest_Z0010.nii warp2d_null0Warp.nii.gz warp2d_00100GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100InverseWarp.nii.gz -R src_Z0010.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00100GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 11/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0011.nii,src_Z0011.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110Warp.nii.gz -R dest_Z0011.nii warp2d_null0Warp.nii.gz warp2d_00110GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110InverseWarp.nii.gz -R src_Z0011.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00110GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 12/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0012.nii,src_Z0012.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120Warp.nii.gz -R dest_Z0012.nii warp2d_null0Warp.nii.gz warp2d_00120GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120InverseWarp.nii.gz -R src_Z0012.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00120GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 13/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0013.nii,src_Z0013.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130Warp.nii.gz -R dest_Z0013.nii warp2d_null0Warp.nii.gz warp2d_00130GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130InverseWarp.nii.gz -R src_Z0013.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00130GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 14/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0014.nii,src_Z0014.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140Warp.nii.gz -R dest_Z0014.nii warp2d_null0Warp.nii.gz warp2d_00140GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140InverseWarp.nii.gz -R src_Z0014.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00140GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 15/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0015.nii,src_Z0015.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150Warp.nii.gz -R dest_Z0015.nii warp2d_null0Warp.nii.gz warp2d_00150GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150InverseWarp.nii.gz -R src_Z0015.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00150GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 16/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0016.nii,src_Z0016.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160Warp.nii.gz -R dest_Z0016.nii warp2d_null0Warp.nii.gz warp2d_00160GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160InverseWarp.nii.gz -R src_Z0016.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00160GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 17/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0017.nii,src_Z0017.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170Warp.nii.gz -R dest_Z0017.nii warp2d_null0Warp.nii.gz warp2d_00170GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170InverseWarp.nii.gz -R src_Z0017.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00170GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 18/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0018.nii,src_Z0018.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180Warp.nii.gz -R dest_Z0018.nii warp2d_null0Warp.nii.gz warp2d_00180GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180InverseWarp.nii.gz -R src_Z0018.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00180GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 19/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0019.nii,src_Z0019.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190Warp.nii.gz -R dest_Z0019.nii warp2d_null0Warp.nii.gz warp2d_00190GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190InverseWarp.nii.gz -R src_Z0019.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00190GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 20/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0020.nii,src_Z0020.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200Warp.nii.gz -R dest_Z0020.nii warp2d_null0Warp.nii.gz warp2d_00200GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200InverseWarp.nii.gz -R src_Z0020.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00200GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
Registering slice 21/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0021.nii,src_Z0021.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210Warp.nii.gz -R dest_Z0021.nii warp2d_null0Warp.nii.gz warp2d_00210GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210InverseWarp.nii.gz -R src_Z0021.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00210GenericAffine.mat # in /tmp/sct-20220920172749.989042-register-5c7xxd6y

Merge warping fields along z...

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220920172749.612429-register-qosxklja
cp step1InverseWarp.nii.gz /tmp/sct-20220920172749.612429-register-qosxklja
rm -rf /tmp/sct-20220920172749.989042-register-5c7xxd6y

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20220920172749.612429-register-qosxklja
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20220920172749.612429-register-qosxklja

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  192 x 192 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n 'BSpline[3]' # in /tmp/sct-20220920172749.612429-register-qosxklja
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  61 x 57 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n 'BSpline[3]' # in /tmp/sct-20220920172749.612429-register-qosxklja
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: t1w_reg.nii.gz
mv /tmp/sct-20220920172749.612429-register-qosxklja/warp_src2dest.nii.gz warp_t1w2mt1_crop.nii.gz
File created: warp_t1w2mt1_crop.nii.gz
File mt1_crop_reg.nii.gz already exists. Deleting it..
File created: mt1_crop_reg.nii.gz
mv /tmp/sct-20220920172749.612429-register-qosxklja/warp_dest2src.nii.gz warp_mt1_crop2t1w.nii.gz
File created: warp_mt1_crop2t1w.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172749.612429-register-qosxklja

Finished! Elapsed time: 10s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_register_multimodal/2022_09_20_172759.613692/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172759.613692.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute MTsat
# Tips: Check your TR and Flip Angle from the Dicom data
sct_compute_mtsat -mt mt1_crop.nii.gz -pd mt0_reg.nii.gz -t1 t1w_reg.nii.gz -trmt 0.030 -trpd 0.030 -trt1 0.015 -famt 9 -fapd 9 -fat1 15

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_compute_mtsat -mt mt1_crop.nii.gz -pd mt0_reg.nii.gz -t1 t1w_reg.nii.gz -trmt 0.030 -trpd 0.030 -trt1 0.015 -famt 9 -fapd 9 -fat1 15
--

Load data...
Compute T1 map...
R1 values were found to be lower than 0.01. They will be set to inf, producing T1=0 for these voxels.
Compute A...
Compute MTsat...
MTsat values were found to be larger than 1. They will be set to zero for these voxels.
Generate output files...
# Extract MTR, T1 and MTsat within the white matter between C2 and C5.
# Tips: Here we use "-discard-neg-val 1" to discard inconsistent negative values in MTR calculation which are caused by noise.
sct_extract_metric -i mtr.nii.gz -method map -o mtr_in_wm.csv -l 51 -vert 2:5

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_extract_metric -i mtr.nii.gz -method map -o mtr_in_wm.csv -l 51 -vert 2:5
--


Load metric image...
Estimation for label: white matter

Done! To view results, type:
xdg-open mtr_in_wm.csv

sct_extract_metric -i mtsat.nii.gz -method map -o mtsat_in_wm.csv -l 51 -vert 2:5

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_extract_metric -i mtsat.nii.gz -method map -o mtsat_in_wm.csv -l 51 -vert 2:5
--


Load metric image...
Estimation for label: white matter

Done! To view results, type:
xdg-open mtsat_in_wm.csv

sct_extract_metric -i t1map.nii.gz -method map -o t1_in_wm.csv -l 51 -vert 2:5

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_extract_metric -i t1map.nii.gz -method map -o t1_in_wm.csv -l 51 -vert 2:5
--


Load metric image...
Estimation for label: white matter

Done! To view results, type:
xdg-open t1_in_wm.csv

# Bring MTR to template space (e.g. for group mapping)
sct_apply_transfo -i mtr.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_mt2template.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_apply_transfo -i mtr.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_mt2template.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  61 x 57 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i mtr.nii.gz -o mtr_reg.nii.gz -t warp_mt2template.nii.gz -r ../../../data/PAM50/template/PAM50_t2.nii.gz -n 'BSpline[3]' # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
Copy affine matrix from destination space to make sure qform/sform are the same.
# Go back to root folder
cd ..


# dmri
# ===========================================================================================
cd dmri
# bring t2 segmentation in dmri space to create mask (no optimization)
sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec bvecs.txt 

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec bvecs.txt
--


Input parameters:
  input file ............dmri.nii.gz
  bvecs file ............bvecs.txt
  bvals file ............
  average ...............1
Creating temporary folder (/tmp/sct-20220920172813.611075-dmri_separate-wztp6pf_)

Copy files into temporary folder...
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/bvecs.txt /tmp/sct-20220920172813.611075-dmri_separate-wztp6pf_/bvecs

Get dimensions data...
.. 96 x 36 x 15 x 35


Identify b=0 and DWI images...
  WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs.
  Transpose bvecs...
  Number of b=0: 5 [0, 31, 32, 33, 34]
  Number of DWI: 30 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]

Split along T dimension...

Merge b=0...

Average b=0...

Average DWI...

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_b0.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_dwi.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_b0_mean.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_dwi_mean.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172813.611075-dmri_separate-wztp6pf_

Finished! Elapsed time: 0s
sct_register_multimodal -i ../t2/t2_seg.nii.gz -d dmri_dwi_mean.nii.gz -identity 1 -x nn

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i ../t2/t2_seg.nii.gz -d dmri_dwi_mean.nii.gz -identity 1 -x nn
--


Input parameters:
  Source .............. ../t2/t2_seg.nii.gz
  Destination ......... dmri_dwi_mean.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920172816.349194-register-zzw_gkt3)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172816.349194-register-zzw_gkt3

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct-20220920172816.349194-register-zzw_gkt3
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct-20220920172816.349194-register-zzw_gkt3

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  64 x 320 x 320 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n NearestNeighbor # in /tmp/sct-20220920172816.349194-register-zzw_gkt3
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  96 x 36 x 15 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n NearestNeighbor # in /tmp/sct-20220920172816.349194-register-zzw_gkt3
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: t2_seg_reg.nii.gz
mv /tmp/sct-20220920172816.349194-register-zzw_gkt3/warp_src2dest.nii.gz warp_t2_seg2dmri_dwi_mean.nii.gz
File created: warp_t2_seg2dmri_dwi_mean.nii.gz
File created: dmri_dwi_mean_reg.nii.gz
mv /tmp/sct-20220920172816.349194-register-zzw_gkt3/warp_dest2src.nii.gz warp_dmri_dwi_mean2t2_seg.nii.gz
File created: warp_dmri_dwi_mean2t2_seg.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172816.349194-register-zzw_gkt3

Finished! Elapsed time: 4s
# create mask to help moco and for faster processing
sct_create_mask -i dmri_dwi_mean.nii.gz -p centerline,t2_seg_reg.nii.gz -size 35mm

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_create_mask -i dmri_dwi_mean.nii.gz -p centerline,t2_seg_reg.nii.gz -size 35mm
--

  OK: t2_seg_reg.nii.gz
Creating temporary folder (/tmp/sct-20220920172822.303251-create_mask-39khlcla)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:228: DeprecationWarning: get_header method is deprecated.
Please use the ``img.header`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:231: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline

Orientation:
  RPI

Dimensions:
(96, 36, 15, 1, 0.8958333, 0.8958333, 5.0, 1)

Create mask...

Remove temporary files...
rm -rf /tmp/sct-20220920172822.303251-create_mask-39khlcla
# crop data
sct_crop_image -i dmri.nii.gz -m mask_dmri_dwi_mean.nii.gz -o dmri_crop.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_crop_image -i dmri.nii.gz -m mask_dmri_dwi_mean.nii.gz -o dmri_crop.nii.gz
--

Bounding box: x=[29, 70], y=[0, 34], z=[0, 15]
Cropping the image...
# motion correction
# Tips: if data have very low SNR you can increase the number of successive images that are averaged into group with "-g". Also see: sct_dmri_moco -h
sct_dmri_moco -i dmri_crop.nii.gz -bvec bvecs.txt

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_dmri_moco -i dmri_crop.nii.gz -bvec bvecs.txt
--


Input parameters:
  Input file ............ dmri_crop.nii.gz
  Group size ............ 3
Creating temporary folder (/tmp/sct-20220920172825.031133-moco-gkcj54zm)

Copying input data to tmp folder and convert to nii...

Get dimensions of data...
  41 x 34 x 15

Data orientation: RPI
  Treated as axial

Set suffix of transformation file name, which depends on the orientation:
Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations

Identify b=0 and DWI images...
  WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs.
  Transpose bvecs...
  Number of b=0: 5 [0, 31, 32, 33, 34]
  Number of DWI: 30 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]

Split along T dimension...

Merge and average b=0 data...

Merge across groups...

-------------------------------------------------------------------------------
  Estimating motion on b=0 images...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ b0.nii
  Reference file ........ data_T0000.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_b0groups

Data dimensions:
  41 x 34 x 15 x 5

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)

-------------------------------------------------------------------------------
  Estimating motion across groups...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ datasub-groups.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_groups

Data dimensions:
  41 x 34 x 15 x 10

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)

-------------------------------------------------------------------------------
  Apply moco
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ data.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. apply
  Mask  ................. 
  Output mat folder ..... mat_final

Data dimensions:
  41 x 34 x 15 x 35

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0000.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0000_moco.nii -t mat_final/mat.Z0000T0000Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0001.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0001_moco.nii -t mat_final/mat.Z0000T0001Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0002.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0002_moco.nii -t mat_final/mat.Z0000T0002Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0003.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0003_moco.nii -t mat_final/mat.Z0000T0003Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0004.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0004_moco.nii -t mat_final/mat.Z0000T0004Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0005.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0005_moco.nii -t mat_final/mat.Z0000T0005Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0006.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0006_moco.nii -t mat_final/mat.Z0000T0006Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0007.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0007_moco.nii -t mat_final/mat.Z0000T0007Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0008.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0008_moco.nii -t mat_final/mat.Z0000T0008Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0009.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0009_moco.nii -t mat_final/mat.Z0000T0009Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0010.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0010_moco.nii -t mat_final/mat.Z0000T0010Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0011.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0011_moco.nii -t mat_final/mat.Z0000T0011Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0012.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0012_moco.nii -t mat_final/mat.Z0000T0012Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0013.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0013_moco.nii -t mat_final/mat.Z0000T0013Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0014.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0014_moco.nii -t mat_final/mat.Z0000T0014Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0015.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0015_moco.nii -t mat_final/mat.Z0000T0015Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0016.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0016_moco.nii -t mat_final/mat.Z0000T0016Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0017.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0017_moco.nii -t mat_final/mat.Z0000T0017Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0018.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0018_moco.nii -t mat_final/mat.Z0000T0018Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0019.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0019_moco.nii -t mat_final/mat.Z0000T0019Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0020.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0020_moco.nii -t mat_final/mat.Z0000T0020Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0021.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0021_moco.nii -t mat_final/mat.Z0000T0021Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0022.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0022_moco.nii -t mat_final/mat.Z0000T0022Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0023.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0023_moco.nii -t mat_final/mat.Z0000T0023Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0024.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0024_moco.nii -t mat_final/mat.Z0000T0024Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0025.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0025_moco.nii -t mat_final/mat.Z0000T0025Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0026.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0026_moco.nii -t mat_final/mat.Z0000T0026Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0027.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0027_moco.nii -t mat_final/mat.Z0000T0027Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0028.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0028_moco.nii -t mat_final/mat.Z0000T0028Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0029.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0029_moco.nii -t mat_final/mat.Z0000T0029Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0030.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0030_moco.nii -t mat_final/mat.Z0000T0030Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0031.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0031_moco.nii -t mat_final/mat.Z0000T0031Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0032.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0032_moco.nii -t mat_final/mat.Z0000T0032Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0033.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0033_moco.nii -t mat_final/mat.Z0000T0033Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0034.nii -o /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_T0034_moco.nii -t mat_final/mat.Z0000T0034Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220920172825.031133-moco-gkcj54zm
Creating temporary folder (/tmp/sct-20220920172838.745073-dmri_separate-xsbod0hk)

File created: /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_moco_b0.nii
File created: /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_moco_dwi.nii
File created: /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_moco_b0_mean.nii
File created: /tmp/sct-20220920172825.031133-moco-gkcj54zm/data_moco_dwi_mean.nii
Extract motion parameters...

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_crop_moco.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_crop_moco_b0_mean.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_crop_moco_dwi_mean.nii.gz
mv moco_params_x.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_x.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_x.nii.gz
mv moco_params_y.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_y.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_y.nii.gz
mv moco_params.tsv /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params.tsv
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params.tsv

Delete temporary files...
rm -rf /tmp/sct-20220920172825.031133-moco-gkcj54zm

Elapsed time: 14s
# segment spinal cord
sct_deepseg_sc -i dmri_crop_moco_dwi_mean.nii.gz -c dwi -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_deepseg_sc -i dmri_crop_moco_dwi_mean.nii.gz -c dwi -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: False
  Kernel dimension: 2d
  Contrast: dwi
  Threshold: 0.01
Creating temporary folder (/tmp/sct-20220920172841.048654-x8i98bf2)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220920172841.073641-cvgxx4wm)
Remove temporary files...
rm -rf /tmp/sct-20220920172841.073641-cvgxx4wm
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Remove temporary files...
rm -rf /tmp/sct-20220920172841.048654-x8i98bf2

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_deepseg_sc/2022_09_20_172841.407355/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172841.407355.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Generate QC for sct_dmri_moco ('dmri_crop_moco_dwi_mean_seg.nii.gz' is needed to align each slice in the QC mosaic)
sct_qc -i dmri_crop.nii.gz -d dmri_crop_moco.nii.gz -s dmri_crop_moco_dwi_mean_seg.nii.gz -p sct_dmri_moco -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_qc -i dmri_crop.nii.gz -d dmri_crop_moco.nii.gz -s dmri_crop_moco_dwi_mean_seg.nii.gz -p sct_dmri_moco -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
Compute center of mass at each slice
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_dmri_moco/2022_09_20_172843.832166/bkg_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_dmri_moco/2022_09_20_172843.832166/overlay_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172843.832166.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register template to dwi
# Tips: Again, here, we prefer to stick to segmentation-based registration. If there are susceptibility distortions in your EPI, then you might consider adding a third step with bsplinesyn or syn transformation for local adjustment.
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t1.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d dmri_crop_moco_dwi_mean.nii.gz -dseg dmri_crop_moco_dwi_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,smooth=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc "$SCT_BP_QC_FOLDER" -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t1.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d dmri_crop_moco_dwi_mean.nii.gz -dseg dmri_crop_moco_dwi_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,smooth=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t1.nii.gz
  Destination ......... dmri_crop_moco_dwi_mean.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920172852.489891-register-0hma3ifd)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920172852.489891-register-0hma3ifd
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... centermass
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220920172854.581351-register-h5f214i_)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 41 x 34 x 15
  voxel size: 0.8958333mm x 0.8958333mm x 15mm

Split input segmentation...

Split destination segmentation...

Generate warping field...
 --> step1Warp.nii.gz

Generate warping field...
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220920172852.489891-register-0hma3ifd
cp step1InverseWarp.nii.gz /tmp/sct-20220920172852.489891-register-0hma3ifd
rm -rf /tmp/sct-20220920172854.581351-register-h5f214i_

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920172852.489891-register-0hma3ifd
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 1
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Generate output files...

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 1mm --restrict-deformation 1x1x0 --output '[step2,src_seg_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920172852.489891-register-0hma3ifd

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220920172852.489891-register-0hma3ifd
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220920172852.489891-register-0hma3ifd

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220920172852.489891-register-0hma3ifd
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  41 x 34 x 15 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220920172852.489891-register-0hma3ifd
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: PAM50_t1_reg.nii.gz
mv /tmp/sct-20220920172852.489891-register-0hma3ifd/warp_src2dest.nii.gz warp_template2dmri.nii.gz
File created: warp_template2dmri.nii.gz
File created: dmri_crop_moco_dwi_mean_reg.nii.gz
mv /tmp/sct-20220920172852.489891-register-0hma3ifd/warp_dest2src.nii.gz warp_dmri2template.nii.gz
File created: warp_dmri2template.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920172852.489891-register-0hma3ifd

Finished! Elapsed time: 20s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_register_multimodal/2022_09_20_172912.144887/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172912.144887.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Warp template and white matter atlas
sct_warp_template -d dmri_crop_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_warp_template -d dmri_crop_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
  Destination image ........ dmri_crop_moco_dwi_mean.nii.gz
  Warping field ............ warp_template2dmri.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_warp_template/2022_09_20_172944.173399/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_172944.173399.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute DTI metrics
# Tips: The flag -method "restore" allows you to estimate the tensor with robust fit (see: sct_dmri_compute_dti -h)
sct_dmri_compute_dti -i dmri_crop_moco.nii.gz -bval bvals.txt -bvec bvecs.txt

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_dmri_compute_dti -i dmri_crop_moco.nii.gz -bval bvals.txt -bvec bvecs.txt
--

data.shape (41, 34, 15, 35)
Computing tensor using "standard" method...
Computing metrics...
# Compute FA within right and left lateral corticospinal tracts from slices 2 to 14 using weighted average method
sct_extract_metric -i dti_FA.nii.gz -z 2:14 -method wa -l 4,5 -o fa_in_cst.csv

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_extract_metric -i dti_FA.nii.gz -z 2:14 -method wa -l 4,5 -o fa_in_cst.csv
--


Load metric image...
Estimation for label: WM left lateral corticospinal tract
Estimation for label: WM right lateral corticospinal tract

Done! To view results, type:
xdg-open fa_in_cst.csv

# Bring metric to template space (e.g. for group mapping)
sct_apply_transfo -i dti_FA.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_dmri2template.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_apply_transfo -i dti_FA.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_dmri2template.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  41 x 34 x 15 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dti_FA.nii.gz -o dti_FA_reg.nii.gz -t warp_dmri2template.nii.gz -r ../../../data/PAM50/template/PAM50_t2.nii.gz -n 'BSpline[3]' # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
Copy affine matrix from destination space to make sure qform/sform are the same.
# Go back to root folder
cd ..


# fmri
# ===========================================================================================
cd fmri
# Average all fMRI time series (to be able to do the next step)
sct_maths -i fmri.nii.gz -mean t -o fmri_mean.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_maths -i fmri.nii.gz -mean t -o fmri_mean.nii.gz
--

# Get cord centerline
sct_get_centerline -i fmri_mean.nii.gz -c t2s

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_get_centerline -i fmri_mean.nii.gz -c t2s
--

Creating temporary folder (/tmp/sct-20220920172957.870628-5bkz25pd)
Remove temporary files...
rm -rf /tmp/sct-20220920172957.870628-5bkz25pd
# Create mask around the cord to help motion correction and for faster processing
sct_create_mask -i fmri_mean.nii.gz -p centerline,fmri_mean_centerline.nii.gz -size 35mm

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_create_mask -i fmri_mean.nii.gz -p centerline,fmri_mean_centerline.nii.gz -size 35mm
--

  OK: fmri_mean_centerline.nii.gz
Creating temporary folder (/tmp/sct-20220920172959.299238-create_mask-f0ye87j3)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:228: DeprecationWarning: get_header method is deprecated.
Please use the ``img.header`` property instead.


Orientation:
  RPI

Dimensions:
(128, 28, 25, 1, 1.0, 1.0, 3.0, 1)

Create mask...

Remove temporary files...
rm -rf /tmp/sct-20220920172959.299238-create_mask-f0ye87j3
* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:231: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline
# Crop data
sct_crop_image -i fmri.nii.gz -m mask_fmri_mean.nii.gz -o fmri_crop.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_crop_image -i fmri.nii.gz -m mask_fmri_mean.nii.gz -o fmri_crop.nii.gz
--

Bounding box: x=[46, 83], y=[0, 28], z=[0, 25]
Cropping the image...
# Motion correction
# Tips: Here data have sufficient SNR and there is visible motion between two consecutive scans, so motion correction is more efficient with -g 1 (i.e. not average consecutive scans)
sct_fmri_moco -i fmri_crop.nii.gz -g 1

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_fmri_moco -i fmri_crop.nii.gz -g 1
--


Input parameters:
  Input file ............ fmri_crop.nii.gz
  Group size ............ 1
Creating temporary folder (/tmp/sct-20220920173002.086833-moco-04vp_hgz)

Copying input data to tmp folder and convert to nii...

Get dimensions of data...
  37 x 28 x 25

Data orientation: RPI
  Treated as axial

Set suffix of transformation file name, which depends on the orientation:
Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations

Split along T dimension...

Merge across groups...

-------------------------------------------------------------------------------
  Estimating motion across groups...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ datasub-groups.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 0
  Gradient step ......... 1
  Metric ................ MeanSquares
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_groups

Data dimensions:
  37 x 28 x 25 x 50

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)

-------------------------------------------------------------------------------
  Apply moco
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ data.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 0
  Gradient step ......... 1
  Metric ................ MeanSquares
  Sampling .............. None
  Todo .................. apply
  Mask  ................. 
  Output mat folder ..... mat_final

Data dimensions:
  37 x 28 x 25 x 50

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0000.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0000_moco.nii -t mat_final/mat.Z0000T0000Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0001.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0001_moco.nii -t mat_final/mat.Z0000T0001Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0002.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0002_moco.nii -t mat_final/mat.Z0000T0002Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0003.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0003_moco.nii -t mat_final/mat.Z0000T0003Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0004.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0004_moco.nii -t mat_final/mat.Z0000T0004Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0005.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0005_moco.nii -t mat_final/mat.Z0000T0005Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0006.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0006_moco.nii -t mat_final/mat.Z0000T0006Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0007.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0007_moco.nii -t mat_final/mat.Z0000T0007Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0008.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0008_moco.nii -t mat_final/mat.Z0000T0008Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0009.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0009_moco.nii -t mat_final/mat.Z0000T0009Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0010.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0010_moco.nii -t mat_final/mat.Z0000T0010Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0011.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0011_moco.nii -t mat_final/mat.Z0000T0011Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0012.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0012_moco.nii -t mat_final/mat.Z0000T0012Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0013.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0013_moco.nii -t mat_final/mat.Z0000T0013Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0014.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0014_moco.nii -t mat_final/mat.Z0000T0014Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0015.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0015_moco.nii -t mat_final/mat.Z0000T0015Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0016.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0016_moco.nii -t mat_final/mat.Z0000T0016Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0017.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0017_moco.nii -t mat_final/mat.Z0000T0017Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0018.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0018_moco.nii -t mat_final/mat.Z0000T0018Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0019.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0019_moco.nii -t mat_final/mat.Z0000T0019Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0020.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0020_moco.nii -t mat_final/mat.Z0000T0020Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0021.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0021_moco.nii -t mat_final/mat.Z0000T0021Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0022.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0022_moco.nii -t mat_final/mat.Z0000T0022Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0023.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0023_moco.nii -t mat_final/mat.Z0000T0023Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0024.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0024_moco.nii -t mat_final/mat.Z0000T0024Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0025.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0025_moco.nii -t mat_final/mat.Z0000T0025Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0026.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0026_moco.nii -t mat_final/mat.Z0000T0026Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0027.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0027_moco.nii -t mat_final/mat.Z0000T0027Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0028.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0028_moco.nii -t mat_final/mat.Z0000T0028Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0029.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0029_moco.nii -t mat_final/mat.Z0000T0029Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0030.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0030_moco.nii -t mat_final/mat.Z0000T0030Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0031.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0031_moco.nii -t mat_final/mat.Z0000T0031Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0032.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0032_moco.nii -t mat_final/mat.Z0000T0032Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0033.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0033_moco.nii -t mat_final/mat.Z0000T0033Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0034.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0034_moco.nii -t mat_final/mat.Z0000T0034Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0035.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0035_moco.nii -t mat_final/mat.Z0000T0035Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0036.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0036_moco.nii -t mat_final/mat.Z0000T0036Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0037.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0037_moco.nii -t mat_final/mat.Z0000T0037Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0038.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0038_moco.nii -t mat_final/mat.Z0000T0038Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0039.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0039_moco.nii -t mat_final/mat.Z0000T0039Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0040.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0040_moco.nii -t mat_final/mat.Z0000T0040Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0041.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0041_moco.nii -t mat_final/mat.Z0000T0041Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0042.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0042_moco.nii -t mat_final/mat.Z0000T0042Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0043.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0043_moco.nii -t mat_final/mat.Z0000T0043Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0044.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0044_moco.nii -t mat_final/mat.Z0000T0044Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0045.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0045_moco.nii -t mat_final/mat.Z0000T0045Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0046.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0046_moco.nii -t mat_final/mat.Z0000T0046Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0047.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0047_moco.nii -t mat_final/mat.Z0000T0047Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0048.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0048_moco.nii -t mat_final/mat.Z0000T0048Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0049.nii -o /tmp/sct-20220920173002.086833-moco-04vp_hgz/data_T0049_moco.nii -t mat_final/mat.Z0000T0049Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220920173002.086833-moco-04vp_hgz
Extract motion parameters...

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/fmri_crop_moco.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/fmri_crop_moco_mean.nii.gz
mv moco_params_x.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_x.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_x.nii.gz
mv moco_params_y.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_y.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_y.nii.gz
mv moco_params.tsv /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params.tsv
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params.tsv

Delete temporary files...
rm -rf /tmp/sct-20220920173002.086833-moco-04vp_hgz

Elapsed time: 39s
# Segment spinal cord manually
#   Since these data have very poor cord/CSF contrast, it is difficult to segment the cord properly using sct_deepseg_sc
#   and hence in this case we do it manually. The file is called: fmri_crop_moco_mean_seg_manual.nii.gz
#   There is no command for this step, because the file is included in the 'sct_example_data' dataset.
# Generate QC for sct_fmri_moco ('fmri_crop_moco_mean_seg_manual.nii.gz' is needed to align each slice in the QC mosaic)
sct_qc -i fmri_crop.nii.gz -d fmri_crop_moco.nii.gz -s fmri_crop_moco_mean_seg_manual.nii.gz -p sct_fmri_moco -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_qc -i fmri_crop.nii.gz -d fmri_crop_moco.nii.gz -s fmri_crop_moco_mean_seg_manual.nii.gz -p sct_fmri_moco -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
Compute center of mass at each slice
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/fmri/sct_fmri_moco/2022_09_20_173044.440308/bkg_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/fmri/sct_fmri_moco/2022_09_20_173044.440308/overlay_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_173044.440308.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register template->fmri
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d fmri_crop_moco_mean.nii.gz -dseg fmri_crop_moco_mean_seg_manual.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=5,gradStep=0.5 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc "$SCT_BP_QC_FOLDER" -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d fmri_crop_moco_mean.nii.gz -dseg fmri_crop_moco_mean_seg_manual.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=5,gradStep=0.5 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t2.nii.gz
  Destination ......... fmri_crop_moco_mean.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220920173100.670528-register-36xjtiae)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220920173100.670528-register-36xjtiae
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... seg
  algo ........... slicereg
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 2
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsSliceRegularizedRegistration -t 'Translation[0.5]' -m 'MeanSquares[dest_seg_RPI_crop.nii,src_seg_reg_crop.nii,1,4,None,0.2]' -p 5 -i 10 -f 1 -s 2 -v 1 -o '[step1,src_seg_reg_crop_regStep1.nii]' # in /tmp/sct-20220920173100.670528-register-36xjtiae

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220920173100.670528-register-36xjtiae
Copy affine matrix from destination space to make sure qform/sform are the same.
Registration parameters:
  type ........... im
  algo ........... bsplinesyn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 5
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Generate output files...

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_RPI_pad.nii,src_reg.nii,1,4]' --convergence 5 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step2,src_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220920173100.670528-register-36xjtiae

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220920173100.670528-register-36xjtiae
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220920173100.670528-register-36xjtiae

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220920173100.670528-register-36xjtiae
Copy affine matrix from destination space to make sure qform/sform are the same.

Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  37 x 28 x 25 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220920173100.670528-register-36xjtiae
Copy affine matrix from destination space to make sure qform/sform are the same.

Generate output files...
File created: PAM50_t2_reg.nii.gz
mv /tmp/sct-20220920173100.670528-register-36xjtiae/warp_src2dest.nii.gz warp_template2fmri.nii.gz
File created: warp_template2fmri.nii.gz
File created: fmri_crop_moco_mean_reg.nii.gz
mv /tmp/sct-20220920173100.670528-register-36xjtiae/warp_dest2src.nii.gz warp_fmri2template.nii.gz
File created: warp_fmri2template.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220920173100.670528-register-36xjtiae

Finished! Elapsed time: 40s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/fmri/sct_register_multimodal/2022_09_20_173140.824068/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_20_173140.824068.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Warp template and spinal levels (here we don't need the WM atlas)
sct_warp_template -d fmri_crop_moco_mean.nii.gz -w warp_template2fmri.nii.gz -a 0 -s 1

--
Spinal Cord Toolbox (git-master-464721865ed5f7adbf6a755f8619816c75e8ef75)

sct_warp_template -d fmri_crop_moco_mean.nii.gz -w warp_template2fmri.nii.gz -a 0 -s 1
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
  Destination image ........ fmri_crop_moco_mean.nii.gz
  Warping field ............ warp_template2fmri.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP SPINAL LEVELS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_01.nii.gz -o label/spinal_levels/spinal_level_01.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_02.nii.gz -o label/spinal_levels/spinal_level_02.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_03.nii.gz -o label/spinal_levels/spinal_level_03.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_04.nii.gz -o label/spinal_levels/spinal_level_04.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_05.nii.gz -o label/spinal_levels/spinal_level_05.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_06.nii.gz -o label/spinal_levels/spinal_level_06.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_07.nii.gz -o label/spinal_levels/spinal_level_07.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_08.nii.gz -o label/spinal_levels/spinal_level_08.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_09.nii.gz -o label/spinal_levels/spinal_level_09.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_10.nii.gz -o label/spinal_levels/spinal_level_10.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_11.nii.gz -o label/spinal_levels/spinal_level_11.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_12.nii.gz -o label/spinal_levels/spinal_level_12.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_13.nii.gz -o label/spinal_levels/spinal_level_13.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_14.nii.gz -o label/spinal_levels/spinal_level_14.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_15.nii.gz -o label/spinal_levels/spinal_level_15.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_16.nii.gz -o label/spinal_levels/spinal_level_16.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_17.nii.gz -o label/spinal_levels/spinal_level_17.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_18.nii.gz -o label/spinal_levels/spinal_level_18.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_19.nii.gz -o label/spinal_levels/spinal_level_19.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_20.nii.gz -o label/spinal_levels/spinal_level_20.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/info_label.txt label/spinal_levels
# Note, once you have computed fMRI statistics in the subject's space, you can use
# warp_fmri2template.nii.gz to bring the statistical maps on the template space, for group analysis.

# Go back to sct_example_data -> data -> $SCT_DIR
cd ../../..


# Display results (to easily compare integrity across SCT versions)
# ===========================================================================================
set +v
~~~
Version:         git-master-464721865ed5f7adbf6a755f8619816c75e8ef75
Ran on:          Linux fv-az180-488 5.15.0-1019-azure
Duration:        0hrs 18min 58sec
---
t2/csa_c2c3.csv:     73.87711295363036  [Row 1, MEAN(area)]
t2/csa_pmj.csv:      73.89298021190447  [Row 1, MEAN(area)]
t2s/csa_gm.csv:      12.487834828856178 [Row 4, MEAN(area)]
t2s/csa_wm.csv:      64.93830702088249  [Row 4, MEAN(area)]
mt/mtr_in_wm.csv:    54.37973940532884  [Row 1, MAP()]
dmri/fa_in_cst.csv:  0.7793999418865862 [Row 1, WA()]
dmri/fa_in_cst.csv:  0.7755359512006275 [Row 2, WA()]
~~~
To open Quality Control (QC) report on a web-browser, run the following:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html
##[debug]Finishing: Run batch_processing.sh

Changed text

Open file

##[debug]Evaluating condition for step: 'Run batch_processing.sh'
##[debug]Evaluating: success()
##[debug]Evaluating success:
##[debug]=> true
##[debug]Result: true
##[debug]Starting: Run batch_processing.sh
##[debug]Loading inputs
##[debug]Loading env
Run bash batch_processing.sh
##[debug]Overwrite 'shell' base on job defaults.
##[debug]/usr/bin/bash --noprofile --norc -e -o pipefail /home/runner/work/_temp/15d4fe95-291b-4e49-89f7-372914cddae6.sh

# For full verbose, uncomment the next line
# set -x

# Fetch OS type
if uname -a | grep -i  darwin > /dev/null 2>&1; then
  # OSX
  open_command="open"
elif uname -a | grep -i  linux > /dev/null 2>&1; then
  # Linux
  open_command="xdg-open"
fi

# Check if users wants to use his own data
if [[ -z "$SCT_BP_DOWNLOAD" ]]; then
	SCT_BP_DOWNLOAD=1
fi

# QC folder
if [[ -z "$SCT_BP_QC_FOLDER" ]]; then
	SCT_BP_QC_FOLDER=`pwd`/"qc_example_data"
fi

# Remove QC folder
if [ -z "$SCT_BP_NO_REMOVE_QC" -a -d "$SCT_BP_QC_FOLDER" ]; then
  echo "Removing $SCT_BP_QC_FOLDER folder."
  rm -rf "$SCT_BP_QC_FOLDER"
fi

# get starting time:
start=`date +%s`

# download example data
if [[ "$SCT_BP_DOWNLOAD" == "1" ]]; then
  sct_download_data -d sct_example_data
fi

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_download_data -d sct_example_data
--

Trying URL: https://github.com/spinalcordtoolbox/sct_example_data/releases/download/r20180525/20180525_sct_example_data.zip
Downloading: 20180525_sct_example_data.zip
Creating temporary folder (/tmp/sct-20220921125334.279878-8kt90_xz)
Unzip data to: /tmp/sct-20220921125334.279878-8kt90_xz
Copying data to: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data
Removing temporary folders...
Done!

cd data/sct_example_data


# t2
# ===========================================================================================
cd t2
# Segment spinal cord
sct_deepseg_sc -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_sc -i t2.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t2
  Threshold: 0.7
Creating temporary folder (/tmp/sct-20220921125336.147834-szwr7fof)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220921125346.709574-10y6ss9j)
Remove temporary files...
rm -rf /tmp/sct-20220921125346.709574-10y6ss9j
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Removing small objects above slice #240
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /tmp/sct-20220921125336.147834-szwr7fof

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_deepseg_sc/2022_09_21_125404.933067/bkg_img.png
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/style.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars
  for dir in range(input.ndim)]
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/css
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/main.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/animation.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/yaml.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/filesaver.min.js /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/js
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/f-icon.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyright.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keydown.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyup.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/imgs
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_assets/fonts
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125404.933067.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Tips: If you are not satisfied with the results you can try with another algorithm:
# sct_propseg -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"
# Vertebral labeling
# Tips: for manual initialization of labeling by clicking at disc C2-C3, use flag -initc2
sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Creating temporary folder (/tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg)

Copying input data to tmp folder...

Straighten spinal cord...
Creating temporary folder (/tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz)
Copy files to tmp folder...
Fitting centerline using B-spline approximation
Error on approximation = 1.45 mm
Error on approximation = 0.8 mm
Error on approximation = 0.78 mm
Error on approximation = 0.26 mm
Error on approximation = 0.18 mm
Error on approximation = 0.17 mm
Error on approximation = 0.19 mm
Error on approximation = 0.19 mm
Error on approximation = 0.19 mm
Create the straight space and the safe zone
Length of spinal cord: 195.1824594930412
Size of spinal cord in z direction: 191.2181565315654
Ratio length/size: 1.0207318333854003
Safe zone boundaries (curved space): [-122.38013064855659, 68.83802588300883]
Safe zone boundaries (straight space): [-124.36228212929447, 70.82017736374672]
Pad input volume to account for spinal cord length...
Time to generate centerline: 22.0 ms
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz
Generate output files...
mv /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
File created: ./data_straight.nii
Remove temporary files...
rm -rf /tmp/sct-20220921125407.832323-straighten_spinalcord-jwwiqemz

Resample to 0.5mm isotropic...
load data...

Apply straightening to segmentation...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -o segmentation_straight.nii -t warp_curve2straight.nii.gz -r data_straightr.nii -n Linear # in /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg
File /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/segmentation_straight.nii already exists. Will overwrite it.

Create label to identify disc...
Creating temporary folder...
Creating temporary folder (/tmp/sct-20220921125447.708364-pjxkarw0)
Run C2-C3 detector...
C2-C3 detected...
Remove temporary files...
rm -rf /tmp/sct-20220921125447.708364-pjxkarw0
File /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/labelz.nii.gz already exists. Will overwrite it.

And apply straightening to label...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -o labelz_straight.nii.gz -t warp_curve2straight.nii.gz -r data_straightr.nii -n NearestNeighbor # in /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg

Get z and disc values from straight label...
.. [308, 3]
Look for template...
Path template: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
Open template and vertebral levels...
Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
Z-values for each disc: [963, 938, 907, 870, 833, 800, 769, 735, 692, 646, 600, 551, 500, 449, 396, 342, 289, 231, 168, 104, 79]
Distances between discs (in voxel): [25.0, 31.0, 37.0, 37.0, 33.0, 31.0, 34.0, 43.0, 46.0, 46.0, 49.0, 51.0, 51.0, 53.0, 54.0, 53.0, 58.0, 63.0, 64.0, 25.0]
Detect intervertebral discs...
Current disc: 2 (z=308). Direction: superior
.. Peak found: z=-2 (correlation = 0.5785475132964076)
Current disc: 1 (z=337). Direction: superior
.. correcting factor: 1.0
.. Switching to inferior direction.
Current disc: 3 (z=271). Direction: inferior
.. Peak found: z=-2 (correlation = 0.46669793555686756)
.. correcting factor: 1.0
Current disc: 4 (z=232). Direction: inferior
.. Peak found: z=0 (correlation = 0.4759131092619541)
.. correcting factor: 1.0
Current disc: 5 (z=199). Direction: inferior
.. Peak found: z=1 (correlation = 0.5489915159060484)
.. correcting factor: 0.9924242424242424
Current disc: 6 (z=169). Direction: inferior
.. Peak found: z=-1 (correlation = 0.6413729873029947)
.. correcting factor: 1.0003910068426198
Current disc: 7 (z=134). Direction: inferior
.. Peak found: z=3 (correlation = 0.49551596833735867)
.. correcting factor: 0.9856199566825753
Current disc: 8 (z=95). Direction: inferior
.. Peak found: z=2 (correlation = 0.5102032109234909)
.. correcting factor: 0.9777074711764266
Current disc: 9 (z=52). Direction: inferior
.. Peak found: z=2 (correlation = 0.5204922661088763)
.. correcting factor: 0.9723418633663299
Current disc: 10 (z=9). Direction: inferior
.. Peak found: z=6 (correlation = 0.5201107394731823)
.. correcting factor: 0.9585067770985733
Adding top disc based on adjusted template distance: #0
.. approximate distance: 24

Un-straighten labeling...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -o segmentation_labeled.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg

Cleaning labeled segmentation:
  removing labeled voxels outside segmentation...
Done cleaning.
File /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/segmentation_labeled.nii already exists. Will overwrite it.

Label discs...

Un-straighten labeled discs...

Dilate labels before warping...
Creating temporary folder (/tmp/sct-20220921125455.872708-apply_transfo-9g92khug)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125455.872708-apply_transfo-9g92khug/dilated_data.nii -o segmentation_labeled_disc.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg

Take the center of mass of each registered dilated labels...
File segmentation_labeled_disc.nii already exists. Will overwrite it.

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_seg_labeled.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_seg_labeled_discs.nii.gz
mv /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/warp_curve2straight.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_curve2straight.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_curve2straight.nii.gz
mv /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/warp_straight2curve.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_straight2curve.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_straight2curve.nii.gz
mv /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg/straight_ref.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/straight_ref.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/straight_ref.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921125407.542814-label_vertebrae-ppbdevqg

*** Generate Quality Control (QC) html report ***
Resample images to NonexNone mm
QcImage: layout with Sagittal slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_label_vertebrae/2022_09_21_125501.394177/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125501.394177.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/math.py:113: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0. Please use `footprint` instead.
  return dilation(data, selem=_get_selem(shape, size, dim), out=None)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/math.py:113: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0. Please use `footprint` instead.
  return dilation(data, selem=_get_selem(shape, size, dim), out=None)

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Create labels at in the cord at C2 and C5 mid-vertebral levels
sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 2,5 -o labels_vert.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 2,5 -o labels_vert.nii.gz
--

Generating output files...
# Tips: you can also create labels manually using:
# sct_label_utils -i t2.nii.gz -create-viewer 2,5 -o labels_vert.nii.gz
# Register to template
sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels_vert.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels_vert.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Check template files...
  OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz
  OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz
  OK: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz

Check parameters:
  Data:                 t2.nii.gz
  Landmarks:            labels_vert.nii.gz
  Segmentation:         t2_seg.nii.gz
  Path template:        /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Remove temp files:    1

Check input labels...
Creating temporary folder (/tmp/sct-20220921125506.526801-register_to_template-vn_57a1w)

Copying input data to tmp folder and convert to nii...

Generate labels from template vertebral labeling

Check if provided labels are available in the template

Binarize segmentation

Resample data to 1mm isotropic...
load data...
load data...
To avoid intensity overflow due to convertion to +uint8+, intensity will be rescaled to the maximum quantization scale

Change orientation of input images to RPI...

Straighten the spinal cord using centerline/segmentation...
Creating temporary folder (/tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3)
Copy files to tmp folder...
Create the straight space and the safe zone
Length of spinal cord: 194.86777391248705
Size of spinal cord in z direction: 191.01429026627324
Ratio length/size: 1.0201737976820586
Safe zone boundaries (curved space): [-122.3822868551715, 68.63200341110175]
Safe zone boundaries (straight space): [-124.3090286782784, 70.55874523420866]
Pad input volume to account for spinal cord length...
Time to generate centerline: 18.0 ms
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3
Generate output files...
mv /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
mv /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3/tmp.anat_rigid_warp.nii.gz /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straight.nii.gz
File created: /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straight.nii.gz
Remove temporary files...
rm -rf /tmp/sct-20220921125512.305906-straighten_spinalcord-w4j7vos3
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Remove unused label on template. Keep only label present in the input label image...
File template_label_body.nii.gz already exists. Will overwrite it.

Dilating input labels using 3vox ball radius

Apply straightening to labels...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/label_projected_1mm_rpi_dilate.nii.gz -o /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/label_projected_1mm_rpi_dilate_straight.nii.gz -t warp_curve2straight.nii.gz -r /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Estimate transformation for step #0...
Labels src: [[-0.49785977044107455, -12.840075485893843, 35.579769644543646], [-1.868628377073808, -13.049818470161009, -17.3863725163054]]
Labels dest: [[-0.0, 46.220001220703125, -100.34002685546875], [-0.0, 45.720001220703125, -153.34002685546875]]
Degrees of freedom (dof): Tx_Ty_Tz_Sz
Optimization terminated successfully.
         Current function value: 0.981628
         Iterations: 2
         Function evaluations: 151
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [   0.           45.97000122 -126.84002686]
Translation:
 [[ -1.18324408 -58.9149482  135.93672542]]

Concatenate transformations: curve --> straight --> affine...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_curve2straightAffine.nii.gz -R template.nii straight2templateAffine.txt warp_curve2straight.nii.gz # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Apply transformation...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/data_1mm_rpi.nii -o /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/data_1mm_rpi_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n 'BSpline[3]' # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop.nii.gz -o /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/seg_bin_1mm_rpi_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Crop data in template space (for faster processing)...

Sub-sample in z-direction (for faster processing)...
load data...
load data...
load data...
load data...

Register straight spinal cord to template...
Creating temporary folder (/tmp/sct-20220921125601.018424-register-3bedzwt4)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #1
Registration parameters:
  type ........... imseg
  algo ........... centermassrot
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pcahog
Creating temporary folder (/tmp/sct-20220921125601.262578-register-4w_rhfh5)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 141 x 141 x 97
  voxel size: 0.5mm x 0.5mm x 97mm

Split input segmentation...

Split destination segmentation...

Split input image...

Split destination image...
Switched to method 'hog' for slice: 0
Switched to method 'hog' for slice: 8
Switched to method 'hog' for slice: 14
Switched to method 'hog' for slice: 15
Switched to method 'hog' for slice: 92
Switched to method 'hog' for slice: 93
Switched to method 'hog' for slice: 94
Switched to method 'hog' for slice: 94
Switched to method 'hog' for slice: 95
Switched to method 'hog' for slice: 95
Switched to method 'hog' for slice: 96
Switched to method 'hog' for slice: 96

Generate warping field...
 --> step1Warp.nii.gz

Generate warping field...
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220921125601.018424-register-3bedzwt4
cp step1InverseWarp.nii.gz /tmp/sct-20220921125601.018424-register-3bedzwt4
rm -rf /tmp/sct-20220921125601.262578-register-4w_rhfh5

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921125601.018424-register-3bedzwt4
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 1
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 1mm --restrict-deformation 1x1x0 --output '[step2,src_seg_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921125601.018424-register-3bedzwt4

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz # in /tmp/sct-20220921125601.018424-register-3bedzwt4
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220921125601.018424-register-3bedzwt4

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220921125601.018424-register-3bedzwt4

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220921125601.018424-register-3bedzwt4

Generate output files...
mv /tmp/sct-20220921125601.018424-register-3bedzwt4/src_reg.nii data_1mm_rpi_straightAffine_crop_sub_reg.nii
File created: data_1mm_rpi_straightAffine_crop_sub_reg.nii
mv /tmp/sct-20220921125601.018424-register-3bedzwt4/warp_src2dest.nii.gz warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz
File created: warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz
mv /tmp/sct-20220921125601.018424-register-3bedzwt4/dest_reg.nii template_crop_sub_reg.nii
File created: template_crop_sub_reg.nii
mv /tmp/sct-20220921125601.018424-register-3bedzwt4/warp_dest2src.nii.gz warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz
File created: warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921125601.018424-register-3bedzwt4

Concatenate transformations: anat --> template...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_anat2template.nii.gz -R template.nii warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz warp_curve2straightAffine.nii.gz # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Concatenate transformations: template --> anat...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_template2anat.nii.gz -R data.nii warp_straight2curve.nii.gz -i straight2templateAffine.txt warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i template.nii -o template2anat.nii.gz -t warp_template2anat.nii.gz -r data.nii -n 'BSpline[3]' # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o anat2template.nii.gz -t warp_anat2template.nii.gz -r template.nii -n 'BSpline[3]' # in /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Generate output files...
mv /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/warp_template2anat.nii.gz warp_template2anat.nii.gz
File created: warp_template2anat.nii.gz
mv /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/warp_anat2template.nii.gz warp_anat2template.nii.gz
File created: warp_anat2template.nii.gz
mv /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/template2anat.nii.gz template2anat.nii.gz
File created: template2anat.nii.gz
mv /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/anat2template.nii.gz anat2template.nii.gz
File created: anat2template.nii.gz
File warp_curve2straight.nii.gz already exists. Deleting it..
mv /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
File created: warp_curve2straight.nii.gz
File warp_straight2curve.nii.gz already exists. Deleting it..
mv /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
File created: warp_straight2curve.nii.gz
File straight_ref.nii.gz already exists. Deleting it..
mv /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w/straight_ref.nii.gz straight_ref.nii.gz
File created: straight_ref.nii.gz

Delete temporary files...
rm -rf /tmp/sct-20220921125506.526801-register_to_template-vn_57a1w

Finished! Elapsed time: 201s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_register_to_template/2022_09_21_125833.544194/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125833.544194.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/math.py:113: FutureWarning: `selem` is a deprecated argument name for `dilation`. It will be removed in version 1.0. Please use `footprint` instead.

  return dilation(data, selem=_get_selem(shape, size, dim), out=None)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars
  for dir in range(input.ndim)]
To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Tips: If you are not satisfied with the results, you can tweak registration parameters.
# For example here, we would like to take into account the rotation of the cord, as well as
# adding a 3rd registration step that uses the image intensity (not only cord segmentations).
# so we could do something like this:
# sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2s.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d t2s.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=seg,algo=slicereg,smooth=3:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz
# Warp template without the white matter atlas (we don't need it at this point)
sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
  Destination image ........ t2.nii.gz
  Warping field ............ warp_template2anat.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template
# Compute cross-sectional area (and other morphometry measures) for each slice
sct_process_segmentation -i t2_seg.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_process_segmentation -i t2_seg.nii.gz
--


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/csa.csv

# Compute cross-sectional area and average between C2 and C3 levels
sct_process_segmentation -i t2_seg.nii.gz -vert 2:3 -o csa_c2c3.csv

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_process_segmentation -i t2_seg.nii.gz -vert 2:3 -o csa_c2c3.csv
--


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/csa_c2c3.csv

# Compute cross-sectionnal area based on distance from pontomedullary junction (PMJ)
# Detect PMJ
sct_detect_pmj -i t2.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER" 

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_detect_pmj -i t2.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Creating temporary folder (/tmp/sct-20220921125929.964002-9kuxa_km)
cp t2.nii.gz /tmp/sct-20220921125929.964002-9kuxa_km
Bounding box: x=[0, 320], y=[0, 320], z=[32, 34]
Cropping the image...

Run PMJ detector
['isct_spine_detect', '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models/t2_model', 't2_midSag', 't2_map_pmj']

Ponto-Medullary Junction detected
.. Peak found: x=-4 (correlation = 0.5729094434043677)
R-L coordinate adjusted from 32 to  28)
Bounding box: x=[0, 320], y=[0, 320], z=[28, 30]
Cropping the image...
File t2_midSag.nii already exists. Will overwrite it.

Run PMJ detector
['isct_spine_detect', '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models/t2_model', 't2_midSag', 't2_map_pmj.nii']

Ponto-Medullary Junction detected
	x_pmj = 35
	y_pmj = 151
	z_pmj = 259

Save resulting file...
cp /tmp/sct-20220921125929.964002-9kuxa_km/t2_pmj.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/t2_pmj.nii.gz
rm -rf /tmp/sct-20220921125929.964002-9kuxa_km

*** Generate Quality Control (QC) html report ***
Resample images to NonexNone mm
QcImage: layout with Sagittal slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_detect_pmj/2022_09_21_125932.994620/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125932.994620.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute cross-section area at 60 mm from PMJ averaged on a 30 mm extent
sct_process_segmentation -i t2_seg.nii.gz -pmj t2_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -qc "$SCT_BP_QC_FOLDER" -qc-image t2.nii.gz -o csa_pmj.csv

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_process_segmentation -i t2_seg.nii.gz -pmj t2_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data -qc-image t2.nii.gz -o csa_pmj.csv
--

Creating temporary folder (/tmp/sct-20220921125937.616292-awjmtbup)

*** Generate Quality Control (QC) html report ***
Resample images to NonexNone mm
QcImage: layout with Sagittal slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2/sct_process_segmentation/2022_09_21_125938.956750/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125938.956750.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/csa_pmj.csv

# Go back to root folder
cd ..


# t2s (stands for t2-star)
# ===========================================================================================
cd t2s
# Spinal cord segmentation
sct_deepseg_sc -i t2s.nii.gz -c t2s -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_sc -i t2s.nii.gz -c t2s -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: False
  Kernel dimension: 2d
  Contrast: t2s
  Threshold: 0.89
Creating temporary folder (/tmp/sct-20220921125941.544279-f67lf6rq)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220921125942.631086-oavo8jbn)
Remove temporary files...
rm -rf /tmp/sct-20220921125942.631086-oavo8jbn
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Removing small objects above slice #30
Remove temporary files...
rm -rf /tmp/sct-20220921125941.544279-f67lf6rq

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2s/sct_deepseg_sc/2022_09_21_125945.831491/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_125945.831491.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars

  for dir in range(input.ndim)]
To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Segment gray matter
sct_deepseg_gm -i t2s.nii.gz -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_gm -i t2s.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/t2s/sct_deepseg_gm/2022_09_21_130005.992322/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_130005.992322.json
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/scipy/ndimage/measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

  for dir in range(input.ndim)]
# Register template->t2s (using warping field generated from template<->t2 registration)
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2s.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d t2s.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,algo=syn,slicewise=1,iter=1,metric=CC -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2s.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d t2s.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,algo=syn,slicewise=1,iter=1,metric=CC -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t2s.nii.gz
  Destination ......... t2s.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921130009.135688-register-22eozink)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921130009.135688-register-22eozink
Registration parameters:
  type ........... seg
  algo ........... centermass
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220921130012.014966-register-agoqq0xp)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 320 x 320 x 32
  voxel size: 0.5mm x 0.5mm x 32mm

Split input segmentation...

Split destination segmentation...
Slice #0 is empty. It will be ignored.
Slice #1 is empty. It will be ignored.
Slice #31 is empty. It will be ignored.

Generate warping field...
 --> step1Warp.nii.gz

Generate warping field...
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220921130009.135688-register-22eozink
cp step1InverseWarp.nii.gz /tmp/sct-20220921130009.135688-register-22eozink
rm -rf /tmp/sct-20220921130012.014966-register-agoqq0xp

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921130009.135688-register-22eozink
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 1
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220921130024.798730-register-z5fpwkd9)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 320 x 320 x 32
  voxel size: 0.5mm x 0.5mm x 32mm

Split input volume...

Split destination volume...
Registering slice 0/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 1/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 2/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 3/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 4/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 5/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 6/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 7/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 8/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 9/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 10/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 11/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 12/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 13/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 14/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 15/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 16/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 17/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 18/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 19/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 20/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 21/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 22/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0022.nii,src_Z0022.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0022,src_Z0022_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 23/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0023.nii,src_Z0023.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0023,src_Z0023_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 24/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0024.nii,src_Z0024.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0024,src_Z0024_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 25/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0025.nii,src_Z0025.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0025,src_Z0025_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 26/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0026.nii,src_Z0026.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0026,src_Z0026_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 27/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0027.nii,src_Z0027.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0027,src_Z0027_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 28/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0028.nii,src_Z0028.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0028,src_Z0028_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 29/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0029.nii,src_Z0029.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0029,src_Z0029_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 30/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0030.nii,src_Z0030.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0030,src_Z0030_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9
Registering slice 31/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0031.nii,src_Z0031.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0031,src_Z0031_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130024.798730-register-z5fpwkd9

Merge warping fields along z...

Move warping fields...
cp step2Warp.nii.gz /tmp/sct-20220921130009.135688-register-22eozink
cp step2InverseWarp.nii.gz /tmp/sct-20220921130009.135688-register-22eozink
rm -rf /tmp/sct-20220921130024.798730-register-z5fpwkd9

--
ESTIMATE TRANSFORMATION FOR STEP #3

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220921130009.135688-register-22eozink
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 1
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220921130119.125074-register-zpdu4u1f)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 320 x 320 x 32
  voxel size: 0.5mm x 0.5mm x 32mm

Split input volume...

Split destination volume...
Registering slice 0/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 1/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 2/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 3/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 4/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 5/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 6/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 7/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 8/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 9/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 10/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 11/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 12/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 13/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 14/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 15/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 16/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 17/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 18/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 19/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 20/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 21/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 22/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0022.nii,src_Z0022.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0022,src_Z0022_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 23/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0023.nii,src_Z0023.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0023,src_Z0023_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 24/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0024.nii,src_Z0024.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0024,src_Z0024_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 25/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0025.nii,src_Z0025.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0025,src_Z0025_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 26/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0026.nii,src_Z0026.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0026,src_Z0026_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 27/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0027.nii,src_Z0027.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0027,src_Z0027_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 28/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0028.nii,src_Z0028.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0028,src_Z0028_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 29/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0029.nii,src_Z0029.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0029,src_Z0029_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 30/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0030.nii,src_Z0030.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0030,src_Z0030_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f
Registering slice 31/31...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'SyN[0.5,3,0]' --metric 'CC[dest_Z0031.nii,src_Z0031.nii,1,4]' --convergence 1 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0031,src_Z0031_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130119.125074-register-zpdu4u1f

Merge warping fields along z...

Move warping fields...
cp step3Warp.nii.gz /tmp/sct-20220921130009.135688-register-22eozink
cp step3InverseWarp.nii.gz /tmp/sct-20220921130009.135688-register-22eozink
rm -rf /tmp/sct-20220921130119.125074-register-zpdu4u1f

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_3.nii.gz warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220921130009.135688-register-22eozink
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz warp_inverse_3.nii.gz # in /tmp/sct-20220921130009.135688-register-22eozink

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220921130009.135688-register-22eozink

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220921130009.135688-register-22eozink

Generate output files...
File created: PAM50_t2s_reg.nii.gz
mv /tmp/sct-20220921130009.135688-register-22eozink/warp_src2dest.nii.gz warp_template2t2s.nii.gz
File created: warp_template2t2s.nii.gz
File created: t2s_reg.nii.gz
mv /tmp/sct-20220921130009.135688-register-22eozink/warp_dest2src.nii.gz warp_t2s2template.nii.gz
File created: warp_t2s2template.nii.gz
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/registration/algorithms.py:1443: RuntimeWarning: Mean of empty slice.

Remove temporary files...
rm -rf /tmp/sct-20220921130009.135688-register-22eozink

Finished! Elapsed time: 110s
  centermass = coordsrc.mean(0)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:182: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:263: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims, where=where)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in true_divide
  subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/registration/algorithms.py:1443: RuntimeWarning: Mean of empty slice.
  centermass = coordsrc.mean(0)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:182: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:263: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims, where=where)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in true_divide
  subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/registration/algorithms.py:1443: RuntimeWarning: Mean of empty slice.
  centermass = coordsrc.mean(0)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:182: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:263: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims, where=where)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in true_divide
  subok=False)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
# Warp template
sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
  Destination image ........ t2s.nii.gz
  Warping field ............ warp_template2t2s.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2t2s.nii.gz -r t2s.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas
# Subtract GM segmentation from cord segmentation to obtain WM segmentation
sct_maths -i t2s_seg.nii.gz -sub t2s_gmseg.nii.gz -o t2s_wmseg.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_maths -i t2s_seg.nii.gz -sub t2s_gmseg.nii.gz -o t2s_wmseg.nii.gz
--

# Compute cross-sectional area of the gray and white matter between C2 and C5
sct_process_segmentation -i t2s_wmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_wm.csv

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_process_segmentation -i t2s_wmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_wm.csv
--


Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s/csa_wm.csv

sct_process_segmentation -i t2s_gmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_gm.csv

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_process_segmentation -i t2s_gmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_gm.csv
--


No properties for slice: 3

Done! To view results, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2s/csa_gm.csv

# OPTIONAL: Update template registration using information from gray matter segmentation
# # <<<
# # Register WM/GM template to WM/GM seg
# sct_register_multimodal -i ../../../data/PAM50/template/PAM50_wm.nii.gz -d t2s_wmseg.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=im,algo=syn,slicewise=1,iter=5 -initwarp warp_template2t2s.nii.gz -initwarpinv warp_t2s2template.nii.gz -qc "$SCT_BP_QC_FOLDER" -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz
# # Warp template (this time corrected for internal structure)
# sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz
# # >>>
cd ..


# t1
# ===========================================================================================
cd t1
# Contrast-agnostic registration
# 1. t1w preprocessing (cropping around spinal cord)
sct_deepseg_sc -i t1.nii.gz -c t1 -centerline cnn

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_sc -i t1.nii.gz -c t1 -centerline cnn
--

Config deepseg_sc:
  Centerline algorithm: cnn
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t1
  Threshold: 0.15
Creating temporary folder (/tmp/sct-20220921130347.677653-rhzhhw_t)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
To avoid intensity overflow due to convertion to +uint8+, intensity will be rescaled to the maximum quantization scale
Brain section detected.
Creating temporary folder (/tmp/sct-20220921130417.827842-1d503a6v)
Remove temporary files...
rm -rf /tmp/sct-20220921130417.827842-1d503a6v
Cropping brain section.
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /tmp/sct-20220921130347.677653-rhzhhw_t
sct_create_mask -i t1.nii.gz -p centerline,t1_seg.nii.gz -size 35mm -f cylinder -o mask_t1.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_create_mask -i t1.nii.gz -p centerline,t1_seg.nii.gz -size 35mm -f cylinder -o mask_t1.nii.gz
--

  OK: t1_seg.nii.gz
Creating temporary folder (/tmp/sct-20220921130442.748382-create_mask-ad7ui90i)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:230: DeprecationWarning: get_header method is deprecated.

Please use the ``img.header`` property instead.
Orientation:

  LPI
* deprecated from version: 2.1

* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
Dimensions:
  hdr = centerline.get_header()  # get header
(192, 260, 320, 1, 0.9999965, 1.0, 1.0, 1)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:233: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).


Create mask...
* deprecated from version: 3.0

* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
Remove temporary files...
  data_centerline = centerline.get_data()  # get centerline
rm -rf /tmp/sct-20220921130442.748382-create_mask-ad7ui90i
sct_crop_image -i t1.nii.gz -m mask_t1.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_crop_image -i t1.nii.gz -m mask_t1.nii.gz
--

Bounding box: x=[72, 114], y=[57, 124], z=[0, 174]
Cropping the image...
# 2. t2w preprocessing (cropping around spinal cord)
cp ../t2/t2.nii.gz ./t2.nii.gz
sct_deepseg_sc -i t2.nii.gz -c t2

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_sc -i t2.nii.gz -c t2
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t2
  Threshold: 0.7
Creating temporary folder (/tmp/sct-20220921130448.094350-p65331wm)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220921130458.631983-ortp8951)
Remove temporary files...
rm -rf /tmp/sct-20220921130458.631983-ortp8951
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Removing small objects above slice #240
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /tmp/sct-20220921130448.094350-p65331wm
sct_create_mask -i t2.nii.gz -p centerline,t2_seg.nii.gz -size 35mm -f cylinder -o mask_t2.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_create_mask -i t2.nii.gz -p centerline,t2_seg.nii.gz -size 35mm -f cylinder -o mask_t2.nii.gz
--

  OK: t2_seg.nii.gz
Creating temporary folder (/tmp/sct-20220921130514.965111-create_mask-00kkkuoj)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:230: DeprecationWarning: get_header method is deprecated.

Orientation:
  LPI

Dimensions:
(64, 320, 320, 1, 0.8000004, 0.8, 0.8, 1)

Create mask...

Remove temporary files...
rm -rf /tmp/sct-20220921130514.965111-create_mask-00kkkuoj
Please use the ``img.header`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:233: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline
sct_crop_image -i t2.nii.gz -m mask_t2.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_crop_image -i t2.nii.gz -m mask_t2.nii.gz
--

Bounding box: x=[8, 56], y=[71, 161], z=[0, 240]
Cropping the image...
# 3. Perform registration
sct_register_multimodal -i t1_crop.nii.gz -d t2_crop.nii.gz -param step=1,type=im,algo=dl

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i t1_crop.nii.gz -d t2_crop.nii.gz -param step=1,type=im,algo=dl
--


Input parameters:
  Source .............. t1_crop.nii.gz
  Destination ......... t2_crop.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921130519.544926-register-d6rkpjup)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130519.544926-register-d6rkpjup

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220921130519.544926-register-d6rkpjup
Registration parameters:
  type ........... im
  algo ........... dl
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Preprocess data by setting an isotropic resolution of 1mm and bringing the source image into same space as moving image...
load data...
Creating temporary folder (/tmp/sct-20220921130521.379350-register-rm0oeqkg)

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct-20220921130521.379350-register-rm0oeqkg
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct-20220921130521.379350-register-rm0oeqkg
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220921130521.379350-register-rm0oeqkg
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220921130521.379350-register-rm0oeqkg
mv /tmp/sct-20220921130521.379350-register-rm0oeqkg/src_reg.nii src_reg_same_space.nii
File created: src_reg_same_space.nii
mv /tmp/sct-20220921130521.379350-register-rm0oeqkg/warp_src2dest.nii.gz warp_src_reg2dest_RPI_iso_res.nii.gz
File created: warp_src_reg2dest_RPI_iso_res.nii.gz
mv /tmp/sct-20220921130521.379350-register-rm0oeqkg/dest_reg.nii src_reg_same_space_inv.nii
File created: src_reg_same_space_inv.nii
mv /tmp/sct-20220921130521.379350-register-rm0oeqkg/warp_dest2src.nii.gz warp_dest_RPI_iso_res2src_reg.nii.gz
File created: warp_dest_RPI_iso_res2src_reg.nii.gz

Load data to register...

 Creating data tensors...

 Input shape for fixed tensor: torch.Size([1, 1, 48, 80, 192])

 Input shape for moving tensor: torch.Size([1, 1, 48, 80, 192])

 Creating VxmDense models with arguments:

{'inshape': [48, 80, 192], 'int_steps': 5, 'int_downsize': 2, 'unet_half_res': True, 'nb_unet_features': ([256, 256, 256, 256], [256, 256, 256, 256, 256, 256])}

 Loading first VxmDense model...

 Loading second VxmDense model...

 Predicting using first VxmDense model...

 Predicting using second VxmDense model...

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20220921130519.544926-register-d6rkpjup
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20220921130519.544926-register-d6rkpjup

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220921130519.544926-register-d6rkpjup

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220921130519.544926-register-d6rkpjup

Generate output files...
File created: t1_crop_reg.nii.gz
mv /tmp/sct-20220921130519.544926-register-d6rkpjup/warp_src2dest.nii.gz warp_t1_crop2t2_crop.nii.gz
File created: warp_t1_crop2t2_crop.nii.gz
File created: t2_crop_reg.nii.gz
mv /tmp/sct-20220921130519.544926-register-d6rkpjup/warp_dest2src.nii.gz warp_t2_crop2t1_crop.nii.gz
File created: warp_t2_crop2t1_crop.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921130519.544926-register-d6rkpjup

Finished! Elapsed time: 28s

# Other useful utilities
# 1. Smooth spinal cord along superior-inferior axis
sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz
--


Check input arguments...
  Volume to smooth .................. t1.nii.gz
  Centerline ........................ t1_seg.nii.gz
  Sigma (mm) ........................ [0, 0, 3]
  Verbose ........................... 1
Creating temporary folder (/tmp/sct-20220921130555.898742-smooth_spinalcord-vgh9ea0b)

Copying input data to tmp folder and convert to nii...
cp t1.nii.gz /tmp/sct-20220921130555.898742-smooth_spinalcord-vgh9ea0b/anat.nii.gz
cp t1_seg.nii.gz /tmp/sct-20220921130555.898742-smooth_spinalcord-vgh9ea0b/centerline.nii.gz

Orient input volume to RPI orientation...

Orient centerline to RPI orientation...

Straighten the spinal cord using centerline/segmentation...
Creating temporary folder (/tmp/sct-20220921130557.141467-straighten_spinalcord-9w6lrep0)
Copy files to tmp folder...
Fitting centerline using B-spline approximation
Error on approximation = 0.4 mm
Error on approximation = 0.32 mm
Error on approximation = 0.26 mm
Error on approximation = 0.08 mm
Error on approximation = 0.08 mm
Error on approximation = 0.04 mm
Error on approximation = 0.03 mm
Error on approximation = 0.03 mm
Create the straight space and the safe zone
Length of spinal cord: 176.60968855611546
Size of spinal cord in z direction: 173.1710381900656
Ratio length/size: 1.019856959928113
Safe zone boundaries (curved space): [-107.36701470917797, 65.80402348088762]
Safe zone boundaries (straight space): [-109.0863398922029, 67.52334866391256]
Pad input volume to account for spinal cord length...
Time to generate centerline: 16.0 ms
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130557.141467-straighten_spinalcord-9w6lrep0
Generate output files...
mv /tmp/sct-20220921130557.141467-straighten_spinalcord-9w6lrep0/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /tmp/sct-20220921130557.141467-straighten_spinalcord-9w6lrep0/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20220921130557.141467-straighten_spinalcord-9w6lrep0/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
File created: ./anat_rpi_straight.nii
Remove temporary files...
rm -rf /tmp/sct-20220921130557.141467-straighten_spinalcord-9w6lrep0
cp straight_ref.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t1/straight_ref.nii.gz
cp warp_curve2straight.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t1/warp_curve2straight.nii.gz
cp warp_straight2curve.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t1/warp_straight2curve.nii.gz

Smooth the straightened image...

Apply the reversed warping field to get back the curved spinal cord...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i anat_rpi_straight_smooth.nii -o anat_rpi_straight_smooth_curved.nii -t warp_straight2curve.nii.gz -r anat.nii -n 'BSpline[3]' # in /tmp/sct-20220921130555.898742-smooth_spinalcord-vgh9ea0b

Replace zeroed voxels by original image...

Generate output file...
File created: t1_smooth.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921130555.898742-smooth_spinalcord-vgh9ea0b

Finished! Elapsed time: 80s

# 2. Flatten cord in the right-left direction (to make nice figure)
sct_flatten_sagittal -i t1.nii.gz -s t1_seg.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_flatten_sagittal -i t1.nii.gz -s t1_seg.nii.gz
--

# Go back to root folder
cd ..


# mt
# ===========================================================================================
cd mt
# Get centerline from mt1 data
sct_get_centerline -i mt1.nii.gz -c t2

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_get_centerline -i mt1.nii.gz -c t2
--

Creating temporary folder (/tmp/sct-20220921130721.282806-4ql0rnov)
Remove temporary files...
rm -rf /tmp/sct-20220921130721.282806-4ql0rnov
# sct_get_centerline -i mt1.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"
# Create mask
sct_create_mask -i mt1.nii.gz -p centerline,mt1_centerline.nii.gz -size 45mm

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_create_mask -i mt1.nii.gz -p centerline,mt1_centerline.nii.gz -size 45mm
--

  OK: mt1_centerline.nii.gz
Creating temporary folder (/tmp/sct-20220921130723.197630-create_mask-fd532xci)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:230: DeprecationWarning: get_header method is deprecated.

Orientation:
  LPI

Dimensions:
(192, 192, 22, 1, 0.8958333, 0.8958333, 5.000001, 1)

Create mask...

Remove temporary files...
rm -rf /tmp/sct-20220921130723.197630-create_mask-fd532xci
Please use the ``img.header`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:233: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline
# Crop data for faster processing
sct_crop_image -i mt1.nii.gz -m mask_mt1.nii.gz -o mt1_crop.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_crop_image -i mt1.nii.gz -m mask_mt1.nii.gz -o mt1_crop.nii.gz
--

Bounding box: x=[64, 125], y=[62, 119], z=[0, 22]
Cropping the image...
# Segment spinal cord
sct_deepseg_sc -i mt1_crop.nii.gz -c t2 -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_sc -i mt1_crop.nii.gz -c t2 -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t2
  Threshold: 0.7
Creating temporary folder (/tmp/sct-20220921130725.730199-_hai5p6_)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220921130725.794571-ezgfb3db)
Remove temporary files...
rm -rf /tmp/sct-20220921130725.794571-ezgfb3db
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Remove temporary files...
rm -rf /tmp/sct-20220921130725.730199-_hai5p6_

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_deepseg_sc/2022_09_21_130726.758442/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_130726.758442.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register mt0->mt1
# Tips: here we only use rigid transformation because both images have very similar sequence parameters. We don't want to use SyN/BSplineSyN to avoid introducing spurious deformations.
# Tips: here we input -dseg because it is needed by the QC report
sct_register_multimodal -i mt0.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i mt0.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Input parameters:
  Source .............. mt0.nii.gz
  Destination ......... mt1_crop.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921130729.681359-register-ngeh8hzc)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130729.681359-register-ngeh8hzc

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220921130729.681359-register-ngeh8hzc
Registration parameters:
  type ........... im
  algo ........... rigid
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220921130730.112694-register-emvxomqt)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 61 x 57 x 22
  voxel size: 0.8958333mm x 0.8958333mm x 22mm

Split input volume...

Split destination volume...
Registering slice 0/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0000.nii,src_Z0000.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000Warp.nii.gz -R dest_Z0000.nii warp2d_null0Warp.nii.gz warp2d_00000GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000InverseWarp.nii.gz -R src_Z0000.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00000GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 1/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0001.nii,src_Z0001.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010Warp.nii.gz -R dest_Z0001.nii warp2d_null0Warp.nii.gz warp2d_00010GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010InverseWarp.nii.gz -R src_Z0001.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00010GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 2/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0002.nii,src_Z0002.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020Warp.nii.gz -R dest_Z0002.nii warp2d_null0Warp.nii.gz warp2d_00020GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020InverseWarp.nii.gz -R src_Z0002.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00020GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 3/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0003.nii,src_Z0003.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030Warp.nii.gz -R dest_Z0003.nii warp2d_null0Warp.nii.gz warp2d_00030GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030InverseWarp.nii.gz -R src_Z0003.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00030GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 4/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0004.nii,src_Z0004.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040Warp.nii.gz -R dest_Z0004.nii warp2d_null0Warp.nii.gz warp2d_00040GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040InverseWarp.nii.gz -R src_Z0004.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00040GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 5/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0005.nii,src_Z0005.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050Warp.nii.gz -R dest_Z0005.nii warp2d_null0Warp.nii.gz warp2d_00050GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050InverseWarp.nii.gz -R src_Z0005.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00050GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 6/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0006.nii,src_Z0006.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060Warp.nii.gz -R dest_Z0006.nii warp2d_null0Warp.nii.gz warp2d_00060GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060InverseWarp.nii.gz -R src_Z0006.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00060GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 7/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0007.nii,src_Z0007.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070Warp.nii.gz -R dest_Z0007.nii warp2d_null0Warp.nii.gz warp2d_00070GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070InverseWarp.nii.gz -R src_Z0007.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00070GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 8/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0008.nii,src_Z0008.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080Warp.nii.gz -R dest_Z0008.nii warp2d_null0Warp.nii.gz warp2d_00080GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080InverseWarp.nii.gz -R src_Z0008.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00080GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 9/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0009.nii,src_Z0009.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090Warp.nii.gz -R dest_Z0009.nii warp2d_null0Warp.nii.gz warp2d_00090GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090InverseWarp.nii.gz -R src_Z0009.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00090GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 10/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0010.nii,src_Z0010.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100Warp.nii.gz -R dest_Z0010.nii warp2d_null0Warp.nii.gz warp2d_00100GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100InverseWarp.nii.gz -R src_Z0010.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00100GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 11/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0011.nii,src_Z0011.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110Warp.nii.gz -R dest_Z0011.nii warp2d_null0Warp.nii.gz warp2d_00110GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110InverseWarp.nii.gz -R src_Z0011.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00110GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 12/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0012.nii,src_Z0012.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120Warp.nii.gz -R dest_Z0012.nii warp2d_null0Warp.nii.gz warp2d_00120GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120InverseWarp.nii.gz -R src_Z0012.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00120GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 13/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0013.nii,src_Z0013.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130Warp.nii.gz -R dest_Z0013.nii warp2d_null0Warp.nii.gz warp2d_00130GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130InverseWarp.nii.gz -R src_Z0013.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00130GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 14/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0014.nii,src_Z0014.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140Warp.nii.gz -R dest_Z0014.nii warp2d_null0Warp.nii.gz warp2d_00140GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140InverseWarp.nii.gz -R src_Z0014.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00140GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 15/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0015.nii,src_Z0015.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150Warp.nii.gz -R dest_Z0015.nii warp2d_null0Warp.nii.gz warp2d_00150GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150InverseWarp.nii.gz -R src_Z0015.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00150GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 16/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0016.nii,src_Z0016.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160Warp.nii.gz -R dest_Z0016.nii warp2d_null0Warp.nii.gz warp2d_00160GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160InverseWarp.nii.gz -R src_Z0016.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00160GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 17/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0017.nii,src_Z0017.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170Warp.nii.gz -R dest_Z0017.nii warp2d_null0Warp.nii.gz warp2d_00170GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170InverseWarp.nii.gz -R src_Z0017.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00170GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 18/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0018.nii,src_Z0018.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180Warp.nii.gz -R dest_Z0018.nii warp2d_null0Warp.nii.gz warp2d_00180GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180InverseWarp.nii.gz -R src_Z0018.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00180GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 19/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0019.nii,src_Z0019.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190Warp.nii.gz -R dest_Z0019.nii warp2d_null0Warp.nii.gz warp2d_00190GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190InverseWarp.nii.gz -R src_Z0019.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00190GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 20/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0020.nii,src_Z0020.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200Warp.nii.gz -R dest_Z0020.nii warp2d_null0Warp.nii.gz warp2d_00200GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200InverseWarp.nii.gz -R src_Z0020.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00200GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
Registering slice 21/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0021.nii,src_Z0021.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210Warp.nii.gz -R dest_Z0021.nii warp2d_null0Warp.nii.gz warp2d_00210GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210InverseWarp.nii.gz -R src_Z0021.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00210GenericAffine.mat # in /tmp/sct-20220921130730.112694-register-emvxomqt

Merge warping fields along z...

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220921130729.681359-register-ngeh8hzc
cp step1InverseWarp.nii.gz /tmp/sct-20220921130729.681359-register-ngeh8hzc
rm -rf /tmp/sct-20220921130730.112694-register-emvxomqt

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20220921130729.681359-register-ngeh8hzc
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20220921130729.681359-register-ngeh8hzc

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n 'BSpline[3]' # in /tmp/sct-20220921130729.681359-register-ngeh8hzc

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n 'BSpline[3]' # in /tmp/sct-20220921130729.681359-register-ngeh8hzc

Generate output files...
File created: mt0_reg.nii.gz
mv /tmp/sct-20220921130729.681359-register-ngeh8hzc/warp_src2dest.nii.gz warp_mt02mt1_crop.nii.gz
File created: warp_mt02mt1_crop.nii.gz
File created: mt1_crop_reg.nii.gz
mv /tmp/sct-20220921130729.681359-register-ngeh8hzc/warp_dest2src.nii.gz warp_mt1_crop2mt0.nii.gz
File created: warp_mt1_crop2mt0.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921130729.681359-register-ngeh8hzc

Finished! Elapsed time: 10s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_register_multimodal/2022_09_21_130739.773792/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_130739.773792.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register template->mt1
# Tips: here we only use the segmentations due to poor SC/CSF contrast at the bottom slice.
# Tips: First step: slicereg based on images, with large smoothing to capture potential motion between anat and mt, then at second step: bpslinesyn in order to adapt the shape of the cord to the mt modality (in case there are distortions between anat and mt).
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=seg,algo=slicereg,smooth=3:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2mt.nii.gz -owarpinv warp_mt2template.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=seg,algo=slicereg,smooth=3:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2mt.nii.gz -owarpinv warp_mt2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t2.nii.gz
  Destination ......... mt1_crop.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921130742.882115-register-z3aa_llh)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921130742.882115-register-z3aa_llh
Registration parameters:
  type ........... seg
  algo ........... slicereg
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 3
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsSliceRegularizedRegistration -t 'Translation[0.5]' -m 'MeanSquares[dest_seg_RPI_crop.nii,src_seg_reg_crop.nii,1,4,None,0.2]' -p 5 -i 10 -f 1 -s 3 -v 1 -o '[step1,src_seg_reg_crop_regStep1.nii]' # in /tmp/sct-20220921130742.882115-register-z3aa_llh

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921130742.882115-register-z3aa_llh
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 1
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220921130747.863292-register-smty_7_r)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 61 x 57 x 22
  voxel size: 0.8958333mm x 0.8958333mm x 22mm

Split input volume...

Split destination volume...
Registering slice 0/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 1/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 2/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 3/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 4/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 5/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 6/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 7/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 8/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 9/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 10/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 11/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 12/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 13/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 14/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 15/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 16/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 17/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 18/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 19/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 20/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r
Registering slice 21/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130747.863292-register-smty_7_r

Merge warping fields along z...

Move warping fields...
cp step2Warp.nii.gz /tmp/sct-20220921130742.882115-register-z3aa_llh
cp step2InverseWarp.nii.gz /tmp/sct-20220921130742.882115-register-z3aa_llh
rm -rf /tmp/sct-20220921130747.863292-register-smty_7_r

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220921130742.882115-register-z3aa_llh
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220921130742.882115-register-z3aa_llh

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220921130742.882115-register-z3aa_llh

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220921130742.882115-register-z3aa_llh

Generate output files...
File created: PAM50_t2_reg.nii.gz
mv /tmp/sct-20220921130742.882115-register-z3aa_llh/warp_src2dest.nii.gz warp_template2mt.nii.gz
File created: warp_template2mt.nii.gz
File mt1_crop_reg.nii.gz already exists. Deleting it..
File created: mt1_crop_reg.nii.gz
mv /tmp/sct-20220921130742.882115-register-z3aa_llh/warp_dest2src.nii.gz warp_mt2template.nii.gz
File created: warp_mt2template.nii.gz

# Warp template
Remove temporary files...
rm -rf /tmp/sct-20220921130742.882115-register-z3aa_llh

Finished! Elapsed time: 23s
sct_warp_template -d mt1_crop.nii.gz -w warp_template2mt.nii.gz -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_warp_template -d mt1_crop.nii.gz -w warp_template2mt.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
  Destination image ........ mt1_crop.nii.gz
  Warping field ............ warp_template2mt.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2mt.nii.gz -r mt1_crop.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_warp_template/2022_09_21_130841.330425/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_130841.330425.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute mtr
sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1_crop.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1_crop.nii.gz
--


Compute MTR...
Found 0 voxels with value=0. These will be replaced by nan.
Threshold to clip values: +/- 100
# Register t1w->mt1
# Tips: We do not need to crop the t1w image before registration because step=0 of the registration is to put the source image in the space of the destination image (equivalent to cropping the t1w)
sct_register_multimodal -i t1w.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc "$SCT_BP_QC_FOLDER"

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Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i t1w.nii.gz -d mt1_crop.nii.gz -dseg mt1_crop_seg.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
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Input parameters:
  Source .............. t1w.nii.gz
  Destination ......... mt1_crop.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921130844.751402-register-2puzl4wh)

Copying input data to tmp folder and convert to nii...

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ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130844.751402-register-2puzl4wh

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ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220921130844.751402-register-2puzl4wh
Registration parameters:
  type ........... im
  algo ........... rigid
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220921130845.128457-register-bh5g01hl)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 61 x 57 x 22
  voxel size: 0.8958333mm x 0.8958333mm x 22mm

Split input volume...

Split destination volume...
Registering slice 0/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0000.nii,src_Z0000.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000Warp.nii.gz -R dest_Z0000.nii warp2d_null0Warp.nii.gz warp2d_00000GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00000InverseWarp.nii.gz -R src_Z0000.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00000GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 1/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0001.nii,src_Z0001.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010Warp.nii.gz -R dest_Z0001.nii warp2d_null0Warp.nii.gz warp2d_00010GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00010InverseWarp.nii.gz -R src_Z0001.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00010GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 2/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0002.nii,src_Z0002.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020Warp.nii.gz -R dest_Z0002.nii warp2d_null0Warp.nii.gz warp2d_00020GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00020InverseWarp.nii.gz -R src_Z0002.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00020GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 3/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0003.nii,src_Z0003.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030Warp.nii.gz -R dest_Z0003.nii warp2d_null0Warp.nii.gz warp2d_00030GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00030InverseWarp.nii.gz -R src_Z0003.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00030GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 4/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0004.nii,src_Z0004.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040Warp.nii.gz -R dest_Z0004.nii warp2d_null0Warp.nii.gz warp2d_00040GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00040InverseWarp.nii.gz -R src_Z0004.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00040GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 5/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0005.nii,src_Z0005.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050Warp.nii.gz -R dest_Z0005.nii warp2d_null0Warp.nii.gz warp2d_00050GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00050InverseWarp.nii.gz -R src_Z0005.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00050GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 6/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0006.nii,src_Z0006.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060Warp.nii.gz -R dest_Z0006.nii warp2d_null0Warp.nii.gz warp2d_00060GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00060InverseWarp.nii.gz -R src_Z0006.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00060GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 7/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0007.nii,src_Z0007.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070Warp.nii.gz -R dest_Z0007.nii warp2d_null0Warp.nii.gz warp2d_00070GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00070InverseWarp.nii.gz -R src_Z0007.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00070GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 8/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0008.nii,src_Z0008.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080Warp.nii.gz -R dest_Z0008.nii warp2d_null0Warp.nii.gz warp2d_00080GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00080InverseWarp.nii.gz -R src_Z0008.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00080GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 9/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0009.nii,src_Z0009.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090Warp.nii.gz -R dest_Z0009.nii warp2d_null0Warp.nii.gz warp2d_00090GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00090InverseWarp.nii.gz -R src_Z0009.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00090GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 10/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0010.nii,src_Z0010.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100Warp.nii.gz -R dest_Z0010.nii warp2d_null0Warp.nii.gz warp2d_00100GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00100InverseWarp.nii.gz -R src_Z0010.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00100GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 11/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0011.nii,src_Z0011.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110Warp.nii.gz -R dest_Z0011.nii warp2d_null0Warp.nii.gz warp2d_00110GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00110InverseWarp.nii.gz -R src_Z0011.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00110GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 12/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0012.nii,src_Z0012.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120Warp.nii.gz -R dest_Z0012.nii warp2d_null0Warp.nii.gz warp2d_00120GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00120InverseWarp.nii.gz -R src_Z0012.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00120GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 13/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0013.nii,src_Z0013.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130Warp.nii.gz -R dest_Z0013.nii warp2d_null0Warp.nii.gz warp2d_00130GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00130InverseWarp.nii.gz -R src_Z0013.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00130GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 14/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0014.nii,src_Z0014.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140Warp.nii.gz -R dest_Z0014.nii warp2d_null0Warp.nii.gz warp2d_00140GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00140InverseWarp.nii.gz -R src_Z0014.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00140GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 15/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0015.nii,src_Z0015.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150Warp.nii.gz -R dest_Z0015.nii warp2d_null0Warp.nii.gz warp2d_00150GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00150InverseWarp.nii.gz -R src_Z0015.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00150GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 16/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0016.nii,src_Z0016.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160Warp.nii.gz -R dest_Z0016.nii warp2d_null0Warp.nii.gz warp2d_00160GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00160InverseWarp.nii.gz -R src_Z0016.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00160GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 17/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0017.nii,src_Z0017.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170Warp.nii.gz -R dest_Z0017.nii warp2d_null0Warp.nii.gz warp2d_00170GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00170InverseWarp.nii.gz -R src_Z0017.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00170GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 18/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0018.nii,src_Z0018.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180Warp.nii.gz -R dest_Z0018.nii warp2d_null0Warp.nii.gz warp2d_00180GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00180InverseWarp.nii.gz -R src_Z0018.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00180GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 19/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0019.nii,src_Z0019.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190Warp.nii.gz -R dest_Z0019.nii warp2d_null0Warp.nii.gz warp2d_00190GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00190InverseWarp.nii.gz -R src_Z0019.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00190GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 20/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0020.nii,src_Z0020.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200Warp.nii.gz -R dest_Z0020.nii warp2d_null0Warp.nii.gz warp2d_00200GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00200InverseWarp.nii.gz -R src_Z0020.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00200GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
Registering slice 21/21...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0021.nii,src_Z0021.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210Warp.nii.gz -R dest_Z0021.nii warp2d_null0Warp.nii.gz warp2d_00210GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 2 warp2d_00210InverseWarp.nii.gz -R src_Z0021.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00210GenericAffine.mat # in /tmp/sct-20220921130845.128457-register-bh5g01hl

Merge warping fields along z...

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220921130844.751402-register-2puzl4wh
cp step1InverseWarp.nii.gz /tmp/sct-20220921130844.751402-register-2puzl4wh
rm -rf /tmp/sct-20220921130845.128457-register-bh5g01hl

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20220921130844.751402-register-2puzl4wh
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20220921130844.751402-register-2puzl4wh

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n 'BSpline[3]' # in /tmp/sct-20220921130844.751402-register-2puzl4wh

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n 'BSpline[3]' # in /tmp/sct-20220921130844.751402-register-2puzl4wh

Generate output files...
File created: t1w_reg.nii.gz
mv /tmp/sct-20220921130844.751402-register-2puzl4wh/warp_src2dest.nii.gz warp_t1w2mt1_crop.nii.gz
File created: warp_t1w2mt1_crop.nii.gz
File mt1_crop_reg.nii.gz already exists. Deleting it..
File created: mt1_crop_reg.nii.gz
mv /tmp/sct-20220921130844.751402-register-2puzl4wh/warp_dest2src.nii.gz warp_mt1_crop2t1w.nii.gz
File created: warp_mt1_crop2t1w.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921130844.751402-register-2puzl4wh

Finished! Elapsed time: 10s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/mt/sct_register_multimodal/2022_09_21_130855.047281/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_130855.047281.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute MTsat
# Tips: Check your TR and Flip Angle from the Dicom data
sct_compute_mtsat -mt mt1_crop.nii.gz -pd mt0_reg.nii.gz -t1 t1w_reg.nii.gz -trmt 0.030 -trpd 0.030 -trt1 0.015 -famt 9 -fapd 9 -fat1 15

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_compute_mtsat -mt mt1_crop.nii.gz -pd mt0_reg.nii.gz -t1 t1w_reg.nii.gz -trmt 0.030 -trpd 0.030 -trt1 0.015 -famt 9 -fapd 9 -fat1 15
--

Load data...
Compute T1 map...
R1 values were found to be lower than 0.01. They will be set to inf, producing T1=0 for these voxels.
Compute A...
Compute MTsat...
MTsat values were found to be larger than 1. They will be set to zero for these voxels.
Generate output files...
# Extract MTR, T1 and MTsat within the white matter between C2 and C5.
# Tips: Here we use "-discard-neg-val 1" to discard inconsistent negative values in MTR calculation which are caused by noise.
sct_extract_metric -i mtr.nii.gz -method map -o mtr_in_wm.csv -l 51 -vert 2:5

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_extract_metric -i mtr.nii.gz -method map -o mtr_in_wm.csv -l 51 -vert 2:5
--


Load metric image...
Estimation for label: white matter

Done! To view results, type:
xdg-open mtr_in_wm.csv

sct_extract_metric -i mtsat.nii.gz -method map -o mtsat_in_wm.csv -l 51 -vert 2:5

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_extract_metric -i mtsat.nii.gz -method map -o mtsat_in_wm.csv -l 51 -vert 2:5
--


Load metric image...
Estimation for label: white matter

Done! To view results, type:
xdg-open mtsat_in_wm.csv

sct_extract_metric -i t1map.nii.gz -method map -o t1_in_wm.csv -l 51 -vert 2:5

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_extract_metric -i t1map.nii.gz -method map -o t1_in_wm.csv -l 51 -vert 2:5
--


Load metric image...
Estimation for label: white matter

Done! To view results, type:
xdg-open t1_in_wm.csv

# Bring MTR to template space (e.g. for group mapping)
sct_apply_transfo -i mtr.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_mt2template.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_apply_transfo -i mtr.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_mt2template.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  61 x 57 x 22 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i mtr.nii.gz -o mtr_reg.nii.gz -t warp_mt2template.nii.gz -r ../../../data/PAM50/template/PAM50_t2.nii.gz -n 'BSpline[3]' # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/mt
Copy affine matrix from destination space to make sure qform/sform are the same.
# Go back to root folder
cd ..


# dmri
# ===========================================================================================
cd dmri
# bring t2 segmentation in dmri space to create mask (no optimization)
sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec bvecs.txt 

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec bvecs.txt
--


Input parameters:
  input file ............dmri.nii.gz
  bvecs file ............bvecs.txt
  bvals file ............
  average ...............1
Creating temporary folder (/tmp/sct-20220921130909.599864-dmri_separate-ixyg14yp)

Copy files into temporary folder...
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/bvecs.txt /tmp/sct-20220921130909.599864-dmri_separate-ixyg14yp/bvecs

Get dimensions data...
.. 96 x 36 x 15 x 35


Identify b=0 and DWI images...
  WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs.
  Transpose bvecs...
  Number of b=0: 5 [0, 31, 32, 33, 34]
  Number of DWI: 30 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]

Split along T dimension...

Merge b=0...

Average b=0...

Average DWI...

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_b0.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_dwi.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_b0_mean.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_dwi_mean.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921130909.599864-dmri_separate-ixyg14yp

Finished! Elapsed time: 0s
sct_register_multimodal -i ../t2/t2_seg.nii.gz -d dmri_dwi_mean.nii.gz -identity 1 -x nn

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i ../t2/t2_seg.nii.gz -d dmri_dwi_mean.nii.gz -identity 1 -x nn
--


Input parameters:
  Source .............. ../t2/t2_seg.nii.gz
  Destination ......... dmri_dwi_mean.nii.gz
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921130912.476293-register-x40q_1k_)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130912.476293-register-x40q_1k_

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_0.nii.gz # in /tmp/sct-20220921130912.476293-register-x40q_1k_
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz # in /tmp/sct-20220921130912.476293-register-x40q_1k_

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n NearestNeighbor # in /tmp/sct-20220921130912.476293-register-x40q_1k_

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n NearestNeighbor # in /tmp/sct-20220921130912.476293-register-x40q_1k_

Generate output files...
File created: t2_seg_reg.nii.gz
mv /tmp/sct-20220921130912.476293-register-x40q_1k_/warp_src2dest.nii.gz warp_t2_seg2dmri_dwi_mean.nii.gz
File created: warp_t2_seg2dmri_dwi_mean.nii.gz
File created: dmri_dwi_mean_reg.nii.gz
mv /tmp/sct-20220921130912.476293-register-x40q_1k_/warp_dest2src.nii.gz warp_dmri_dwi_mean2t2_seg.nii.gz
File created: warp_dmri_dwi_mean2t2_seg.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921130912.476293-register-x40q_1k_

Finished! Elapsed time: 5s
# create mask to help moco and for faster processing
sct_create_mask -i dmri_dwi_mean.nii.gz -p centerline,t2_seg_reg.nii.gz -size 35mm

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_create_mask -i dmri_dwi_mean.nii.gz -p centerline,t2_seg_reg.nii.gz -size 35mm
--

  OK: t2_seg_reg.nii.gz
Creating temporary folder (/tmp/sct-20220921130918.744223-create_mask-cpqlm_2k)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:230: DeprecationWarning: get_header method is deprecated.
Please use the ``img.header`` property instead.


Orientation:
* deprecated from version: 2.1
  RPI
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0

  hdr = centerline.get_header()  # get header
Dimensions:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:233: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
(96, 36, 15, 1, 0.8958333, 0.8958333, 5.0, 1)


* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
Create mask...
  data_centerline = centerline.get_data()  # get centerline

Remove temporary files...
rm -rf /tmp/sct-20220921130918.744223-create_mask-cpqlm_2k
# crop data
sct_crop_image -i dmri.nii.gz -m mask_dmri_dwi_mean.nii.gz -o dmri_crop.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_crop_image -i dmri.nii.gz -m mask_dmri_dwi_mean.nii.gz -o dmri_crop.nii.gz
--

Bounding box: x=[29, 70], y=[0, 34], z=[0, 15]
Cropping the image...
# motion correction
# Tips: if data have very low SNR you can increase the number of successive images that are averaged into group with "-g". Also see: sct_dmri_moco -h
sct_dmri_moco -i dmri_crop.nii.gz -bvec bvecs.txt

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_dmri_moco -i dmri_crop.nii.gz -bvec bvecs.txt
--


Input parameters:
  Input file ............ dmri_crop.nii.gz
  Group size ............ 3
Creating temporary folder (/tmp/sct-20220921130921.590449-moco-7hesbj8g)

Copying input data to tmp folder and convert to nii...

Get dimensions of data...
  41 x 34 x 15

Data orientation: RPI
  Treated as axial

Set suffix of transformation file name, which depends on the orientation:
Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations

Identify b=0 and DWI images...
  WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs.
  Transpose bvecs...
  Number of b=0: 5 [0, 31, 32, 33, 34]
  Number of DWI: 30 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]

Split along T dimension...

Merge and average b=0 data...

Merge across groups...

-------------------------------------------------------------------------------
  Estimating motion on b=0 images...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ b0.nii
  Reference file ........ data_T0000.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_b0groups

Data dimensions:
  41 x 34 x 15 x 5

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)

-------------------------------------------------------------------------------
  Estimating motion across groups...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ datasub-groups.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_groups

Data dimensions:
  41 x 34 x 15 x 10

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)

-------------------------------------------------------------------------------
  Apply moco
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ data.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 1
  Gradient step ......... 1
  Metric ................ MI
  Sampling .............. None
  Todo .................. apply
  Mask  ................. 
  Output mat folder ..... mat_final

Data dimensions:
  41 x 34 x 15 x 35

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0000.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0000_moco.nii -t mat_final/mat.Z0000T0000Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0001.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0001_moco.nii -t mat_final/mat.Z0000T0001Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0002.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0002_moco.nii -t mat_final/mat.Z0000T0002Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0003.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0003_moco.nii -t mat_final/mat.Z0000T0003Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0004.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0004_moco.nii -t mat_final/mat.Z0000T0004Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0005.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0005_moco.nii -t mat_final/mat.Z0000T0005Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0006.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0006_moco.nii -t mat_final/mat.Z0000T0006Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0007.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0007_moco.nii -t mat_final/mat.Z0000T0007Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0008.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0008_moco.nii -t mat_final/mat.Z0000T0008Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0009.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0009_moco.nii -t mat_final/mat.Z0000T0009Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0010.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0010_moco.nii -t mat_final/mat.Z0000T0010Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0011.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0011_moco.nii -t mat_final/mat.Z0000T0011Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0012.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0012_moco.nii -t mat_final/mat.Z0000T0012Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0013.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0013_moco.nii -t mat_final/mat.Z0000T0013Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0014.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0014_moco.nii -t mat_final/mat.Z0000T0014Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0015.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0015_moco.nii -t mat_final/mat.Z0000T0015Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0016.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0016_moco.nii -t mat_final/mat.Z0000T0016Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0017.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0017_moco.nii -t mat_final/mat.Z0000T0017Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0018.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0018_moco.nii -t mat_final/mat.Z0000T0018Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0019.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0019_moco.nii -t mat_final/mat.Z0000T0019Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0020.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0020_moco.nii -t mat_final/mat.Z0000T0020Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0021.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0021_moco.nii -t mat_final/mat.Z0000T0021Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0022.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0022_moco.nii -t mat_final/mat.Z0000T0022Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0023.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0023_moco.nii -t mat_final/mat.Z0000T0023Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0024.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0024_moco.nii -t mat_final/mat.Z0000T0024Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0025.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0025_moco.nii -t mat_final/mat.Z0000T0025Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0026.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0026_moco.nii -t mat_final/mat.Z0000T0026Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0027.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0027_moco.nii -t mat_final/mat.Z0000T0027Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0028.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0028_moco.nii -t mat_final/mat.Z0000T0028Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0029.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0029_moco.nii -t mat_final/mat.Z0000T0029Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0030.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0030_moco.nii -t mat_final/mat.Z0000T0030Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0031.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0031_moco.nii -t mat_final/mat.Z0000T0031Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0032.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0032_moco.nii -t mat_final/mat.Z0000T0032Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0033.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0033_moco.nii -t mat_final/mat.Z0000T0033Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0034.nii -o /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_T0034_moco.nii -t mat_final/mat.Z0000T0034Warp.nii.gz -r datasub_0_mean.nii.gz -n 'BSpline[3]' # in /tmp/sct-20220921130921.590449-moco-7hesbj8g
Creating temporary folder (/tmp/sct-20220921130935.507250-dmri_separate-u9ksr8oo)

File created: /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_moco_b0.nii
File created: /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_moco_dwi.nii
File created: /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_moco_b0_mean.nii
File created: /tmp/sct-20220921130921.590449-moco-7hesbj8g/data_moco_dwi_mean.nii
Extract motion parameters...

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_crop_moco.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_crop_moco_b0_mean.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/dmri_crop_moco_dwi_mean.nii.gz
mv moco_params_x.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_x.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_x.nii.gz
mv moco_params_y.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_y.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params_y.nii.gz
mv moco_params.tsv /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params.tsv
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri/moco_params.tsv

Delete temporary files...
rm -rf /tmp/sct-20220921130921.590449-moco-7hesbj8g

Elapsed time: 15s
# segment spinal cord
sct_deepseg_sc -i dmri_crop_moco_dwi_mean.nii.gz -c dwi -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_deepseg_sc -i dmri_crop_moco_dwi_mean.nii.gz -c dwi -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: False
  Kernel dimension: 2d
  Contrast: dwi
  Threshold: 0.01
Creating temporary folder (/tmp/sct-20220921130937.887528-fa1uukbf)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Creating temporary folder (/tmp/sct-20220921130937.913128-ns2gtxri)
Remove temporary files...
rm -rf /tmp/sct-20220921130937.913128-ns2gtxri
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Remove temporary files...
rm -rf /tmp/sct-20220921130937.887528-fa1uukbf

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_deepseg_sc/2022_09_21_130938.254212/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_130938.254212.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Generate QC for sct_dmri_moco ('dmri_crop_moco_dwi_mean_seg.nii.gz' is needed to align each slice in the QC mosaic)
sct_qc -i dmri_crop.nii.gz -d dmri_crop_moco.nii.gz -s dmri_crop_moco_dwi_mean_seg.nii.gz -p sct_dmri_moco -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_qc -i dmri_crop.nii.gz -d dmri_crop_moco.nii.gz -s dmri_crop_moco_dwi_mean_seg.nii.gz -p sct_dmri_moco -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
Compute center of mass at each slice
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_dmri_moco/2022_09_21_130940.780007/bkg_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_dmri_moco/2022_09_21_130940.780007/overlay_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_130940.780007.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register template to dwi
# Tips: Again, here, we prefer to stick to segmentation-based registration. If there are susceptibility distortions in your EPI, then you might consider adding a third step with bsplinesyn or syn transformation for local adjustment.
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t1.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d dmri_crop_moco_dwi_mean.nii.gz -dseg dmri_crop_moco_dwi_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,smooth=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc "$SCT_BP_QC_FOLDER" -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t1.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d dmri_crop_moco_dwi_mean.nii.gz -dseg dmri_crop_moco_dwi_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,smooth=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t1.nii.gz
  Destination ......... dmri_crop_moco_dwi_mean.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921130949.770863-register-f8d8t9ma)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921130949.770863-register-f8d8t9ma
Registration parameters:
  type ........... seg
  algo ........... centermass
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20220921130952.015733-register-gtbrz0oi)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 41 x 34 x 15
  voxel size: 0.8958333mm x 0.8958333mm x 15mm

Split input segmentation...

Split destination segmentation...

Generate warping field...
 --> step1Warp.nii.gz

Generate warping field...
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20220921130949.770863-register-f8d8t9ma
cp step1InverseWarp.nii.gz /tmp/sct-20220921130949.770863-register-f8d8t9ma
rm -rf /tmp/sct-20220921130952.015733-register-gtbrz0oi

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921130949.770863-register-f8d8t9ma
Registration parameters:
  type ........... seg
  algo ........... bsplinesyn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 3
  smooth ......... 1
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 1mm --restrict-deformation 1x1x0 --output '[step2,src_seg_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921130949.770863-register-f8d8t9ma

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220921130949.770863-register-f8d8t9ma
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220921130949.770863-register-f8d8t9ma

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220921130949.770863-register-f8d8t9ma

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220921130949.770863-register-f8d8t9ma

Generate output files...
File created: PAM50_t1_reg.nii.gz
mv /tmp/sct-20220921130949.770863-register-f8d8t9ma/warp_src2dest.nii.gz warp_template2dmri.nii.gz
File created: warp_template2dmri.nii.gz
File created: dmri_crop_moco_dwi_mean_reg.nii.gz
mv /tmp/sct-20220921130949.770863-register-f8d8t9ma/warp_dest2src.nii.gz warp_dmri2template.nii.gz
File created: warp_dmri2template.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921130949.770863-register-f8d8t9ma

Finished! Elapsed time: 21s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_register_multimodal/2022_09_21_131010.444001/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_131010.444001.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Warp template and white matter atlas
sct_warp_template -d dmri_crop_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_warp_template -d dmri_crop_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
  Destination image ........ dmri_crop_moco_dwi_mean.nii.gz
  Warping field ............ warp_template2dmri.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2dmri.nii.gz -r dmri_crop_moco_dwi_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/dmri/sct_warp_template/2022_09_21_131044.680729/bkg_img.png
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_131044.680729.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Compute DTI metrics
# Tips: The flag -method "restore" allows you to estimate the tensor with robust fit (see: sct_dmri_compute_dti -h)
sct_dmri_compute_dti -i dmri_crop_moco.nii.gz -bval bvals.txt -bvec bvecs.txt

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_dmri_compute_dti -i dmri_crop_moco.nii.gz -bval bvals.txt -bvec bvecs.txt
--

data.shape (41, 34, 15, 35)
Computing tensor using "standard" method...
Computing metrics...
# Compute FA within right and left lateral corticospinal tracts from slices 2 to 14 using weighted average method
sct_extract_metric -i dti_FA.nii.gz -z 2:14 -method wa -l 4,5 -o fa_in_cst.csv

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_extract_metric -i dti_FA.nii.gz -z 2:14 -method wa -l 4,5 -o fa_in_cst.csv
--


Load metric image...
Estimation for label: WM left lateral corticospinal tract
Estimation for label: WM right lateral corticospinal tract

Done! To view results, type:
xdg-open fa_in_cst.csv

# Bring metric to template space (e.g. for group mapping)
sct_apply_transfo -i dti_FA.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_dmri2template.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_apply_transfo -i dti_FA.nii.gz -d ../../../data/PAM50/template/PAM50_t2.nii.gz -w warp_dmri2template.nii.gz
--


Parse list of warping fields...

Get dimensions of data...
  41 x 34 x 15 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dti_FA.nii.gz -o dti_FA_reg.nii.gz -t warp_dmri2template.nii.gz -r ../../../data/PAM50/template/PAM50_t2.nii.gz -n 'BSpline[3]' # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/dmri
Copy affine matrix from destination space to make sure qform/sform are the same.
# Go back to root folder
cd ..


# fmri
# ===========================================================================================
cd fmri
# Average all fMRI time series (to be able to do the next step)
sct_maths -i fmri.nii.gz -mean t -o fmri_mean.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_maths -i fmri.nii.gz -mean t -o fmri_mean.nii.gz
--

# Get cord centerline
sct_get_centerline -i fmri_mean.nii.gz -c t2s

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_get_centerline -i fmri_mean.nii.gz -c t2s
--

Creating temporary folder (/tmp/sct-20220921131059.144659-_ktnl052)
Remove temporary files...
rm -rf /tmp/sct-20220921131059.144659-_ktnl052
# Create mask around the cord to help motion correction and for faster processing
sct_create_mask -i fmri_mean.nii.gz -p centerline,fmri_mean_centerline.nii.gz -size 35mm

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_create_mask -i fmri_mean.nii.gz -p centerline,fmri_mean_centerline.nii.gz -size 35mm
--

  OK: fmri_mean_centerline.nii.gz
Creating temporary folder (/tmp/sct-20220921131100.660337-create_mask-74uh6e50)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:230: DeprecationWarning: get_header method is deprecated.
Please use the ``img.header`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_create_mask.py:233: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline

Orientation:
  RPI

Dimensions:
(128, 28, 25, 1, 1.0, 1.0, 3.0, 1)

Create mask...

Remove temporary files...
rm -rf /tmp/sct-20220921131100.660337-create_mask-74uh6e50
# Crop data
sct_crop_image -i fmri.nii.gz -m mask_fmri_mean.nii.gz -o fmri_crop.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_crop_image -i fmri.nii.gz -m mask_fmri_mean.nii.gz -o fmri_crop.nii.gz
--

Bounding box: x=[46, 83], y=[0, 28], z=[0, 25]
Cropping the image...
# Motion correction
# Tips: Here data have sufficient SNR and there is visible motion between two consecutive scans, so motion correction is more efficient with -g 1 (i.e. not average consecutive scans)
sct_fmri_moco -i fmri_crop.nii.gz -g 1

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_fmri_moco -i fmri_crop.nii.gz -g 1
--


Input parameters:
  Input file ............ fmri_crop.nii.gz
  Group size ............ 1
Creating temporary folder (/tmp/sct-20220921131103.597660-moco-qhdp2qsj)

Copying input data to tmp folder and convert to nii...

Get dimensions of data...
  37 x 28 x 25

Data orientation: RPI
  Treated as axial

Set suffix of transformation file name, which depends on the orientation:
Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations

Split along T dimension...

Merge across groups...

-------------------------------------------------------------------------------
  Estimating motion across groups...
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ datasub-groups.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 0
  Gradient step ......... 1
  Metric ................ MeanSquares
  Sampling .............. None
  Todo .................. estimate_and_apply
  Mask  ................. 
  Output mat folder ..... mat_groups

Data dimensions:
  37 x 28 x 25 x 50

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)

-------------------------------------------------------------------------------
  Apply moco
-------------------------------------------------------------------------------

Input parameters:
  Input file ............ data.nii
  Reference file ........ datasub_0_mean.nii.gz
  Polynomial degree ..... 2
  Smoothing kernel ...... 0
  Gradient step ......... 1
  Metric ................ MeanSquares
  Sampling .............. None
  Todo .................. apply
  Mask  ................. 
  Output mat folder ..... mat_final

Data dimensions:
  37 x 28 x 25 x 50

Copy file_target to a temporary file...

Register. Loop across Z (note: there is only one Z if orientation is axial)
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0000.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0000_moco.nii -t mat_final/mat.Z0000T0000Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0001.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0001_moco.nii -t mat_final/mat.Z0000T0001Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0002.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0002_moco.nii -t mat_final/mat.Z0000T0002Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0003.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0003_moco.nii -t mat_final/mat.Z0000T0003Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0004.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0004_moco.nii -t mat_final/mat.Z0000T0004Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0005.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0005_moco.nii -t mat_final/mat.Z0000T0005Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0006.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0006_moco.nii -t mat_final/mat.Z0000T0006Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0007.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0007_moco.nii -t mat_final/mat.Z0000T0007Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0008.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0008_moco.nii -t mat_final/mat.Z0000T0008Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0009.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0009_moco.nii -t mat_final/mat.Z0000T0009Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0010.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0010_moco.nii -t mat_final/mat.Z0000T0010Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0011.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0011_moco.nii -t mat_final/mat.Z0000T0011Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0012.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0012_moco.nii -t mat_final/mat.Z0000T0012Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0013.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0013_moco.nii -t mat_final/mat.Z0000T0013Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0014.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0014_moco.nii -t mat_final/mat.Z0000T0014Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0015.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0015_moco.nii -t mat_final/mat.Z0000T0015Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0016.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0016_moco.nii -t mat_final/mat.Z0000T0016Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0017.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0017_moco.nii -t mat_final/mat.Z0000T0017Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0018.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0018_moco.nii -t mat_final/mat.Z0000T0018Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0019.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0019_moco.nii -t mat_final/mat.Z0000T0019Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0020.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0020_moco.nii -t mat_final/mat.Z0000T0020Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0021.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0021_moco.nii -t mat_final/mat.Z0000T0021Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0022.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0022_moco.nii -t mat_final/mat.Z0000T0022Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0023.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0023_moco.nii -t mat_final/mat.Z0000T0023Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0024.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0024_moco.nii -t mat_final/mat.Z0000T0024Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0025.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0025_moco.nii -t mat_final/mat.Z0000T0025Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0026.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0026_moco.nii -t mat_final/mat.Z0000T0026Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0027.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0027_moco.nii -t mat_final/mat.Z0000T0027Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0028.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0028_moco.nii -t mat_final/mat.Z0000T0028Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0029.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0029_moco.nii -t mat_final/mat.Z0000T0029Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0030.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0030_moco.nii -t mat_final/mat.Z0000T0030Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0031.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0031_moco.nii -t mat_final/mat.Z0000T0031Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0032.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0032_moco.nii -t mat_final/mat.Z0000T0032Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0033.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0033_moco.nii -t mat_final/mat.Z0000T0033Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0034.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0034_moco.nii -t mat_final/mat.Z0000T0034Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0035.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0035_moco.nii -t mat_final/mat.Z0000T0035Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0036.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0036_moco.nii -t mat_final/mat.Z0000T0036Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0037.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0037_moco.nii -t mat_final/mat.Z0000T0037Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0038.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0038_moco.nii -t mat_final/mat.Z0000T0038Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0039.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0039_moco.nii -t mat_final/mat.Z0000T0039Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0040.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0040_moco.nii -t mat_final/mat.Z0000T0040Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0041.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0041_moco.nii -t mat_final/mat.Z0000T0041Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0042.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0042_moco.nii -t mat_final/mat.Z0000T0042Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0043.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0043_moco.nii -t mat_final/mat.Z0000T0043Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0044.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0044_moco.nii -t mat_final/mat.Z0000T0044Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0045.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0045_moco.nii -t mat_final/mat.Z0000T0045Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0046.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0046_moco.nii -t mat_final/mat.Z0000T0046Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0047.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0047_moco.nii -t mat_final/mat.Z0000T0047Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0048.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0048_moco.nii -t mat_final/mat.Z0000T0048Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0049.nii -o /tmp/sct-20220921131103.597660-moco-qhdp2qsj/data_T0049_moco.nii -t mat_final/mat.Z0000T0049Warp.nii.gz -r datasub_0_mean.nii.gz -n Linear # in /tmp/sct-20220921131103.597660-moco-qhdp2qsj
Extract motion parameters...

Generate output files...
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/fmri_crop_moco.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/fmri_crop_moco_mean.nii.gz
mv moco_params_x.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_x.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_x.nii.gz
mv moco_params_y.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_y.nii.gz
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params_y.nii.gz
mv moco_params.tsv /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params.tsv
File created: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri/moco_params.tsv

Delete temporary files...
rm -rf /tmp/sct-20220921131103.597660-moco-qhdp2qsj

Elapsed time: 39s
# Segment spinal cord manually
#   Since these data have very poor cord/CSF contrast, it is difficult to segment the cord properly using sct_deepseg_sc
#   and hence in this case we do it manually. The file is called: fmri_crop_moco_mean_seg_manual.nii.gz
#   There is no command for this step, because the file is included in the 'sct_example_data' dataset.
# Generate QC for sct_fmri_moco ('fmri_crop_moco_mean_seg_manual.nii.gz' is needed to align each slice in the QC mosaic)
sct_qc -i fmri_crop.nii.gz -d fmri_crop_moco.nii.gz -s fmri_crop_moco_mean_seg_manual.nii.gz -p sct_fmri_moco -qc "$SCT_BP_QC_FOLDER"

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_qc -i fmri_crop.nii.gz -d fmri_crop_moco.nii.gz -s fmri_crop_moco_mean_seg_manual.nii.gz -p sct_fmri_moco -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data
--


*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
Compute center of mass at each slice
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/fmri/sct_fmri_moco/2022_09_21_131146.519990/bkg_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Saving gif /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/fmri/sct_fmri_moco/2022_09_21_131146.519990/overlay_img.gif
Animation.save using <class 'matplotlib.animation.PillowWriter'>
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_131146.519990.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Register template->fmri
sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d fmri_crop_moco_mean.nii.gz -dseg fmri_crop_moco_mean_seg_manual.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=5,gradStep=0.5 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc "$SCT_BP_QC_FOLDER" -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_register_multimodal -i ../../../data/PAM50/template/PAM50_t2.nii.gz -iseg ../../../data/PAM50/template/PAM50_cord.nii.gz -d fmri_crop_moco_mean.nii.gz -dseg fmri_crop_moco_mean_seg_manual.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=5,gradStep=0.5 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz
--


Input parameters:
  Source .............. ../../../data/PAM50/template/PAM50_t2.nii.gz
  Destination ......... fmri_crop_moco_mean.nii.gz
  Init transfo ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20220921131203.252107-register-hwuuneun)

Copying input data to tmp folder and convert to nii...

Skip step=0 and replace with initial transformations: 
  /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20220921131203.252107-register-hwuuneun
Registration parameters:
  type ........... seg
  algo ........... slicereg
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 2
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsSliceRegularizedRegistration -t 'Translation[0.5]' -m 'MeanSquares[dest_seg_RPI_crop.nii,src_seg_reg_crop.nii,1,4,None,0.2]' -p 5 -i 10 -f 1 -s 2 -v 1 -o '[step1,src_seg_reg_crop_regStep1.nii]' # in /tmp/sct-20220921131203.252107-register-hwuuneun

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20220921131203.252107-register-hwuuneun
Registration parameters:
  type ........... im
  algo ........... bsplinesyn
  slicewise ...... 0
  metric ......... MeanSquares
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 5
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_RPI_pad.nii,src_reg.nii,1,4]' --convergence 5 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step2,src_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20220921131203.252107-register-hwuuneun

Concatenate transformations...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_template2anat.nii.gz # in /tmp/sct-20220921131203.252107-register-hwuuneun
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20220921131203.252107-register-hwuuneun

Apply transfo source --> dest...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20220921131203.252107-register-hwuuneun

Apply transfo dest --> source...
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20220921131203.252107-register-hwuuneun

Generate output files...
File created: PAM50_t2_reg.nii.gz
mv /tmp/sct-20220921131203.252107-register-hwuuneun/warp_src2dest.nii.gz warp_template2fmri.nii.gz
File created: warp_template2fmri.nii.gz
File created: fmri_crop_moco_mean_reg.nii.gz
mv /tmp/sct-20220921131203.252107-register-hwuuneun/warp_dest2src.nii.gz warp_fmri2template.nii.gz
File created: warp_fmri2template.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20220921131203.252107-register-hwuuneun

Finished! Elapsed time: 41s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/data/sct_example_data/fmri/sct_register_multimodal/2022_09_21_131244.377421/bkg_img.png
Mask type float64
Successfully generated the QC results in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/_json/qc_2022_09_21_131244.377421.json

To see the results in a browser, type:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html

# Warp template and spinal levels (here we don't need the WM atlas)
sct_warp_template -d fmri_crop_moco_mean.nii.gz -w warp_template2fmri.nii.gz -a 0 -s 1

--
Spinal Cord Toolbox (git-HEAD-45931667989081e9b001d483c1452bcdcfff0060)

sct_warp_template -d fmri_crop_moco_mean.nii.gz -w warp_template2fmri.nii.gz -a 0 -s 1
--


Check parameters:
  Working directory ........ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
  Destination image ........ fmri_crop_moco_mean.nii.gz
  Warping field ............ warp_template2fmri.nii.gz
  Path template ............ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n NearestNeighbor # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP SPINAL LEVELS:
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_01.nii.gz -o label/spinal_levels/spinal_level_01.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_02.nii.gz -o label/spinal_levels/spinal_level_02.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_03.nii.gz -o label/spinal_levels/spinal_level_03.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_04.nii.gz -o label/spinal_levels/spinal_level_04.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_05.nii.gz -o label/spinal_levels/spinal_level_05.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_06.nii.gz -o label/spinal_levels/spinal_level_06.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_07.nii.gz -o label/spinal_levels/spinal_level_07.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_08.nii.gz -o label/spinal_levels/spinal_level_08.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_09.nii.gz -o label/spinal_levels/spinal_level_09.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_10.nii.gz -o label/spinal_levels/spinal_level_10.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_11.nii.gz -o label/spinal_levels/spinal_level_11.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_12.nii.gz -o label/spinal_levels/spinal_level_12.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_13.nii.gz -o label/spinal_levels/spinal_level_13.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_14.nii.gz -o label/spinal_levels/spinal_level_14.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_15.nii.gz -o label/spinal_levels/spinal_level_15.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_16.nii.gz -o label/spinal_levels/spinal_level_16.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_17.nii.gz -o label/spinal_levels/spinal_level_17.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_18.nii.gz -o label/spinal_levels/spinal_level_18.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_19.nii.gz -o label/spinal_levels/spinal_level_19.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_20.nii.gz -o label/spinal_levels/spinal_level_20.nii.gz -t warp_template2fmri.nii.gz -r fmri_crop_moco_mean.nii.gz -n Linear # in /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/sct_example_data/fmri
cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50/spinal_levels/info_label.txt label/spinal_levels
# Note, once you have computed fMRI statistics in the subject's space, you can use
# warp_fmri2template.nii.gz to bring the statistical maps on the template space, for group analysis.

# Go back to sct_example_data -> data -> $SCT_DIR
cd ../../..


# Display results (to easily compare integrity across SCT versions)
# ===========================================================================================
set +v
~~~
Version:         git-HEAD-45931667989081e9b001d483c1452bcdcfff0060
Ran on:          Linux fv-az133-414 5.15.0-1019-azure
Duration:        0hrs 19min 34sec
---
t2/csa_c2c3.csv:     73.87711295363036  [Row 1, MEAN(area)]
t2/csa_pmj.csv:      73.89298021190447  [Row 1, MEAN(area)]
t2s/csa_gm.csv:      12.487834828856178 [Row 4, MEAN(area)]
t2s/csa_wm.csv:      64.93830702088249  [Row 4, MEAN(area)]
mt/mtr_in_wm.csv:    54.37973940532884  [Row 1, MAP()]
dmri/fa_in_cst.csv:  0.7793999418865862 [Row 1, WA()]
dmri/fa_in_cst.csv:  0.7755359512006275 [Row 2, WA()]
~~~
To open Quality Control (QC) report on a web-browser, run the following:
xdg-open /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/qc_example_data/index.html
##[debug]Finishing: Run batch_processing.sh