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Test run vs. joshua's run

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joshua@master >

$ /path/to/sct_7.3/bin/sct_warp_template -d /path/to/sct_7.3/data/sct_testing_data/mt/mt1.nii.gz -w /path/to/sct_7.3/data/sct_testing_data/mt/warp_template2mt.nii.gz -a 1 -qc qc

$ [~/repos/sct_tutorial_data/single_subject/data/mt] # sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc qc

Spinal Cord Toolbox (git-jn/3508-parallel-tutorial-testing-de628019e07e1c39a0da293794c35d6d4dfcf364)

Spinal Cord Toolbox (7.3)

sct_warp_template -d /path/to/sct_7.3/data/sct_testing_data/mt/mt1.nii.gz -w /path/to/sct_7.3/data/sct_testing_data/mt/warp_template2mt.nii.gz -a 1 -qc qc

sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc qc

Check parameters:

Working directory ........ /home/joshua/repos/sct_tutorial_data/single_subject/data/mt

Working directory ........ /path/to

Destination image ........ mt1.nii.gz

Destination image ........ /path/to/sct_7.3/data/sct_testing_data/mt/mt1.nii.gz

Warping field ............ warp_template2mt.nii.gz

Warping field ............ /path/to/sct_7.3/data/sct_testing_data/mt/warp_template2mt.nii.gz

Path template ............ /home/joshua/repos/spinalcordtoolbox/data/PAM50

Path template ............ /path/to/sct_7.3/data/PAM50

Output folder ............ label

WARP TEMPLATE:

File label/template/PAM50_t1.nii.gz already exists. Will overwrite it.

File label/template/PAM50_t2.nii.gz already exists. Will overwrite it.

File label/template/PAM50_t2s.nii.gz already exists. Will overwrite it.

File label/template/PAM50_cord.nii.gz already exists. Will overwrite it.

File label/template/PAM50_wm.nii.gz already exists. Will overwrite it.

File label/template/PAM50_gm.nii.gz already exists. Will overwrite it.

File label/template/PAM50_csf.nii.gz already exists. Will overwrite it.

File label/template/PAM50_levels.nii.gz already exists. Will overwrite it.

File label/template/PAM50_levels_continuous.nii.gz already exists. Will overwrite it.

File label/template/PAM50_label_body.nii.gz already exists. Will overwrite it.

File label/template/PAM50_label_disc.nii.gz already exists. Will overwrite it.

File label/template/PAM50_label_discPosterior.nii.gz already exists. Will overwrite it.

File label/template/PAM50_spine.nii.gz already exists. Will overwrite it.

File label/template/PAM50_centerline.nii.gz already exists. Will overwrite it.

File label/template/PAM50_spinal_midpoint.nii.gz already exists. Will overwrite it.

File label/template/PAM50_spinal_levels.nii.gz already exists. Will overwrite it.

File label/template/PAM50_rootlets.nii.gz already exists. Will overwrite it.

File label/template/PAM50_rootlets_midpoint.nii.gz already exists. Will overwrite it.

cp /home/joshua/repos/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

cp /path/to/sct_7.3/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:

File label/atlas/PAM50_atlas_00.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_01.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_02.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_03.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_04.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_05.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_06.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_07.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_08.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_09.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_10.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_11.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_12.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_13.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_14.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_15.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_16.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_17.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_18.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_19.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_20.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_21.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_22.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_23.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_24.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_25.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_26.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_27.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_28.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_29.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_30.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_31.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_32.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_33.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_34.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_35.nii.gz already exists. Will overwrite it.

File label/atlas/PAM50_atlas_36.nii.gz already exists. Will overwrite it.

cp /home/joshua/repos/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas

cp /path/to/sct_7.3/data/PAM50/atlas/info_label.txt label/atlas

Resampling image "mt1.nii.gz" to 0.6x0.6 mm

Resampling image "PAM50_wm.nii.gz" to 0.6x0.6 mm

Compute center of mass at each slice

/home/joshua/repos/spinalcordtoolbox/python/envs/venv_sct/lib/python3.10/site-packages/scipy/ndimage/_measurements.py:1548: RuntimeWarning: invalid value encountered in scalar divide

/path/to/sct_7.3/python/envs/venv_sct/lib/python3.10/site-packages/scipy/ndimage/_measurements.py:1548: RuntimeWarning: invalid value encountered in scalar divide

results = [sum_labels(input * grids[dir].astype(float), labels, index) / normalizer

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

/home/joshua/repos/sct_tutorial_data/single_subject/data/mt/qc/single_subject/data/mt/sct_warp_template/2026_06_11_113703.476821/background_img.png

/path/to/qc/data/sct_testing_data/mt/sct_warp_template/2026_06_12_002227.940179/background_img.png

Successfully generated the QC results in /home/joshua/repos/sct_tutorial_data/single_subject/data/mt/qc/_json/qc_2026_06_11_113703.476821.json

Successfully generated the QC results in /path/to/qc/_json/qc_2026_06_12_002227.940179.json

To see the results in a browser, type:

xdg-open /home/joshua/repos/sct_tutorial_data/single_subject/data/mt/qc/index.html

open /path/to/qc/index.html

Done! To view results, type:

fsleyes mt1.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm YlOrRd -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &

fsleyes sct_7.3/data/sct_testing_data/mt/mt1.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm YlOrRd -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &

Total runtime; 91.624 seconds.

Total runtime; 40.047 seconds.

Différences enregistrées

Texte d'origine

Ouvrir un fichier

joshua@master >
$ [~/repos/sct_tutorial_data/single_subject/data/mt] # sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc qc

--
Spinal Cord Toolbox (git-jn/3508-parallel-tutorial-testing-de628019e07e1c39a0da293794c35d6d4dfcf364)

sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc qc
--

Check parameters:
  Working directory ........ /home/joshua/repos/sct_tutorial_data/single_subject/data/mt
  Destination image ........ mt1.nii.gz
  Warping field ............ warp_template2mt.nii.gz
  Path template ............ /home/joshua/repos/spinalcordtoolbox/data/PAM50
  Output folder ............ label

WARP TEMPLATE:
File label/template/PAM50_t1.nii.gz already exists. Will overwrite it.
File label/template/PAM50_t2.nii.gz already exists. Will overwrite it.
File label/template/PAM50_t2s.nii.gz already exists. Will overwrite it.
File label/template/PAM50_cord.nii.gz already exists. Will overwrite it.
File label/template/PAM50_wm.nii.gz already exists. Will overwrite it.
File label/template/PAM50_gm.nii.gz already exists. Will overwrite it.
File label/template/PAM50_csf.nii.gz already exists. Will overwrite it.
File label/template/PAM50_levels.nii.gz already exists. Will overwrite it.
File label/template/PAM50_levels_continuous.nii.gz already exists. Will overwrite it.
File label/template/PAM50_label_body.nii.gz already exists. Will overwrite it.
File label/template/PAM50_label_disc.nii.gz already exists. Will overwrite it.
File label/template/PAM50_label_discPosterior.nii.gz already exists. Will overwrite it.
File label/template/PAM50_spine.nii.gz already exists. Will overwrite it.
File label/template/PAM50_centerline.nii.gz already exists. Will overwrite it.
File label/template/PAM50_spinal_midpoint.nii.gz already exists. Will overwrite it.
File label/template/PAM50_spinal_levels.nii.gz already exists. Will overwrite it.
File label/template/PAM50_rootlets.nii.gz already exists. Will overwrite it.
File label/template/PAM50_rootlets_midpoint.nii.gz already exists. Will overwrite it.
cp /home/joshua/repos/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
File label/atlas/PAM50_atlas_00.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_01.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_02.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_03.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_04.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_05.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_06.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_07.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_08.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_09.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_10.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_11.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_12.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_13.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_14.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_15.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_16.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_17.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_18.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_19.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_20.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_21.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_22.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_23.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_24.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_25.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_26.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_27.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_28.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_29.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_30.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_31.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_32.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_33.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_34.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_35.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_36.nii.gz already exists. Will overwrite it.
cp /home/joshua/repos/spinalcordtoolbox/data/PAM50/atlas/info_label.txt label/atlas
Resampling image "mt1.nii.gz" to 0.6x0.6 mm
Resampling image "PAM50_wm.nii.gz" to 0.6x0.6 mm
Compute center of mass at each slice
/home/joshua/repos/spinalcordtoolbox/python/envs/venv_sct/lib/python3.10/site-packages/scipy/ndimage/_measurements.py:1548: RuntimeWarning: invalid value encountered in scalar divide
  results = [sum_labels(input * grids[dir].astype(float), labels, index) / normalizer

*** Generating Quality Control (QC) html report ***
/home/joshua/repos/sct_tutorial_data/single_subject/data/mt/qc/single_subject/data/mt/sct_warp_template/2026_06_11_113703.476821/background_img.png
Successfully generated the QC results in /home/joshua/repos/sct_tutorial_data/single_subject/data/mt/qc/_json/qc_2026_06_11_113703.476821.json

To see the results in a browser, type:
xdg-open /home/joshua/repos/sct_tutorial_data/single_subject/data/mt/qc/index.html

Done! To view results, type:
fsleyes mt1.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm YlOrRd -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &

Total runtime; 91.624 seconds.

Texte modifié

Ouvrir un fichier

$ /path/to/sct_7.3/bin/sct_warp_template -d /path/to/sct_7.3/data/sct_testing_data/mt/mt1.nii.gz -w /path/to/sct_7.3/data/sct_testing_data/mt/warp_template2mt.nii.gz -a 1 -qc qc
--
Spinal Cord Toolbox (7.3)
sct_warp_template -d /path/to/sct_7.3/data/sct_testing_data/mt/mt1.nii.gz -w /path/to/sct_7.3/data/sct_testing_data/mt/warp_template2mt.nii.gz -a 1 -qc qc
--

Check parameters:
Working directory ........ /path/to
Destination image ........ /path/to/sct_7.3/data/sct_testing_data/mt/mt1.nii.gz
Warping field ............ /path/to/sct_7.3/data/sct_testing_data/mt/warp_template2mt.nii.gz
Path template ............ /path/to/sct_7.3/data/PAM50
Output folder ............ label

WARP TEMPLATE:
File label/template/PAM50_t1.nii.gz already exists. Will overwrite it.
File label/template/PAM50_t2.nii.gz already exists. Will overwrite it.
File label/template/PAM50_t2s.nii.gz already exists. Will overwrite it.
File label/template/PAM50_cord.nii.gz already exists. Will overwrite it.
File label/template/PAM50_wm.nii.gz already exists. Will overwrite it.
File label/template/PAM50_gm.nii.gz already exists. Will overwrite it.
File label/template/PAM50_csf.nii.gz already exists. Will overwrite it.
File label/template/PAM50_levels.nii.gz already exists. Will overwrite it.
File label/template/PAM50_levels_continuous.nii.gz already exists. Will overwrite it.
File label/template/PAM50_label_body.nii.gz already exists. Will overwrite it.
File label/template/PAM50_label_disc.nii.gz already exists. Will overwrite it.
File label/template/PAM50_label_discPosterior.nii.gz already exists. Will overwrite it.
File label/template/PAM50_spine.nii.gz already exists. Will overwrite it.
File label/template/PAM50_centerline.nii.gz already exists. Will overwrite it.
File label/template/PAM50_spinal_midpoint.nii.gz already exists. Will overwrite it.
File label/template/PAM50_spinal_levels.nii.gz already exists. Will overwrite it.
File label/template/PAM50_rootlets.nii.gz already exists. Will overwrite it.
File label/template/PAM50_rootlets_midpoint.nii.gz already exists. Will overwrite it.
cp /path/to/sct_7.3/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
File label/atlas/PAM50_atlas_00.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_01.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_02.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_03.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_04.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_05.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_06.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_07.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_08.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_09.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_10.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_11.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_12.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_13.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_14.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_15.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_16.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_17.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_18.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_19.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_20.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_21.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_22.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_23.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_24.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_25.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_26.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_27.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_28.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_29.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_30.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_31.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_32.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_33.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_34.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_35.nii.gz already exists. Will overwrite it.
File label/atlas/PAM50_atlas_36.nii.gz already exists. Will overwrite it.
cp /path/to/sct_7.3/data/PAM50/atlas/info_label.txt label/atlas
Resampling image "mt1.nii.gz" to 0.6x0.6 mm
Resampling image "PAM50_wm.nii.gz" to 0.6x0.6 mm
Compute center of mass at each slice
/path/to/sct_7.3/python/envs/venv_sct/lib/python3.10/site-packages/scipy/ndimage/_measurements.py:1548: RuntimeWarning: invalid value encountered in scalar divide
  results = [sum_labels(input * grids[dir].astype(float), labels, index) / normalizer

*** Generating Quality Control (QC) html report ***
/path/to/qc/data/sct_testing_data/mt/sct_warp_template/2026_06_12_002227.940179/background_img.png
Successfully generated the QC results in /path/to/qc/_json/qc_2026_06_12_002227.940179.json

To see the results in a browser, type:
open /path/to/qc/index.html

Done! To view results, type:
fsleyes sct_7.3/data/sct_testing_data/mt/mt1.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm YlOrRd -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &

Total runtime; 40.047 seconds.