nameT2 = '3D-T2W-S' %file4SCT{2};
pathQC = '/Users/Akash/CanProCo/Processed/Edmonton/M0/CAN-05-PPM-067-M0/3D-T2W-S/QC'
fprintf('+ Runing SCT segmentation function \n')
tic
sctLABEL = ['/Users/Akash/sct_4.2.2/bin/sct_label_vertebrae -i ' fileT2 ' -s ' fileT2_seg ' -c t2 -qc ' pathQC];
fprintf('2/7.- sct_label_vertebrae\n')
[a2, b2] = unix(sctLABEL)
fprintf('\b (%.2fmin)\n', toc/60) ~~~
**Command Window Output:**
pathT2 =
'/Users/Akash/CanProCo/Processed/Edmonton/M0/CAN-05-PPM-067-M0/3D-T2W-S/'
nameT2 =
'3D-T2W-S'
pathQC =
'/Users/Akash/CanProCo/Processed/Edmonton/M0/CAN-05-PPM-067-M0/3D-T2W-S/QC'
+ Runing SCT segmentation function
2/7.- sct_label_vertebrae
a2 =
1
b2 =
'
--
Spinal Cord Toolbox (4.2.2)
Folder /Users/Akash/CanProCo/Processed/Edmonton/M0/CAN-05-PPM-067-M0/3D-T2W-S/QC has been created.
e[0m
Create temporary folder (/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519130324.394102-label_vertebrae-6jn_rx0h)...e[0m
e[0m
Copying input data to tmp folder...e[0m
e[0m
Straighten spinal cord...e[0m
e[0m
Create temporary folder (/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519130324.745956-straighten_spinalcord-8h4lae44)...e[0m
e[0m
Copy files to tmp folder...e[0m
e[33mWindow length needs to be >= 3. Returning input signal.e[0m
e[33mWindow length needs to be >= 3. Returning input signal.e[0m
Fitting centerline using B-spline approximation
Error on approximation = 2.78 mm
Error on approximation = 0.26 mm
Error on approximation = 0.55 mm
Error on approximation = 0.31 mm
Error on approximation = 0.08 mm
Error on approximation = 0.08 mm
Error on approximation = 0.06 mm
Error on approximation = 0.04 mm
Error on approximation = 0.04 mm
Error on approximation = 0.03 mm
Create the straight space and the safe zone
Length of spinal cord: 198.7267781175262
Size of spinal cord in z direction: 190.3342163467316
Ratio length/size: 1.0440938152471013
Safe zone boundaries (curved space): [-144.762688560668, 45.5715277860636]
Safe zone boundaries (straight space): [-148.9589694460653, 49.7678086714609]
Pad input volume to account for spinal cord length...
Time to generate centerline: 25.0 ms
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Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image…
e[94m/Users/Akash/sct_4.2.2/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n ‘BSpline[3]’ # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519130324.745956-straighten_spinalcord-8h4lae44e[0m
Generate output files…
e[0m File created: ./warp_curve2straight.nii.gze[0m
e[0m File created: ./warp_straight2curve.nii.gze[0m
e[94mcp /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519130324.745956-straighten_spinalcord-8h4lae44/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gze[0m
e[94msct_convert -i /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519130324.745956-straighten_spinalcord-8h4lae44/tmp.anat_rigid_warp.nii.gz -o ./data_straight.niie[0m
e[0m File created: ./data_straight.niie[0m
Remove temporary files…
e[94mrm -rf /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519130324.745956-straighten_spinalcord-8h4lae44e[0m
e[0m
Finished! Elapsed time: 41 se[0m
e[0m
Resample to 0.5mm isotropic…e[0m
e[94msct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519130324.394102-label_vertebrae-6jn_rx0he[0m
Traceback (most recent call last):
File “/Users/Akash/sct_4.2.2/scripts/sct_label_vertebrae.py”, line 427, in
main()
File “/Users/Akash/sct_4.2.2/scripts/sct_label_vertebrae.py”, line 266, in main
s, o = sct.run([‘sct_resample’, ‘-i’, ‘data_straight.nii’, ‘-mm’, ‘0.5x0.5x0.5’, ‘-x’, ‘linear’, ‘-o’, ‘data_straightr.nii’], verbose=verbose)
File “/Users/Akash/sct_4.2.2/scripts/sct_utils.py”, line 291, in run
process = subprocess.Popen(cmd, shell=shell, cwd=cwd, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, env=env)
File “/Users/Akash/sct_4.2.2/python/envs/venv_sct/lib/python3.6/subprocess.py”, line 729, in init
restore_signals, start_new_session)
File “/Users/Akash/sct_4.2.2/python/envs/venv_sct/lib/python3.6/subprocess.py”, line 1364, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘sct_resample’: ‘sct_resample’
’
(0.71min)
these are aliases (not actual nifti files)
also, i would need the segmentation file so i can fully reproduce.
I think these should be the correct files, too large to upload so I shared a dropbox link.
Hi,
I could not reproduce the issue. See my QC output: qc-20200519-202739.zip (463.3 KB)
Could you please try this syntax with the files you’ve uploaded, and copy/paste the full output, as well as the output of sct_check_dependencies, in case you encounter an error:
sct_label_vertebrae -i 3D-T2W-S.nii.gz -s 3D-T2W-S_seg.nii.gz -c t2 -qc qc
Best,
Julien
(base) MacBook-Pro-7:3D-T2W-S Akash$ sct_label_vertebrae -i 3D-T2W-S.nii.gz -s 3D-T2W-S_seg.nii.gz -c t2 -qc qc
–
Spinal Cord Toolbox (4.2.2)
Create temporary folder (/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b)…
Copying input data to tmp folder…
Straighten spinal cord…
Create temporary folder (/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.681805-straighten_spinalcord-392zp5eg)…
Copy files to tmp folder…
Window length needs to be >= 3. Returning input signal.
Window length needs to be >= 3. Returning input signal.
Fitting centerline using B-spline approximation
Error on approximation = 30.05 mm
Error on approximation = 4.22 mm
Error on approximation = 3.36 mm
Error on approximation = 1.67 mm
Error on approximation = 0.59 mm
Error on approximation = 0.31 mm
Error on approximation = 0.24 mm
Error on approximation = 0.22 mm
Error on approximation = 0.19 mm
Error on approximation = 0.19 mm
Error on approximation = 0.15 mm
Error on approximation = 0.14 mm
Error on approximation = 0.12 mm
Error on approximation = 0.11 mm
Error on approximation = 0.1 mm
Error on approximation = 0.11 mm
Error on approximation = 0.11 mm
Error on approximation = 0.1 mm
Create the straight space and the safe zone
Length of spinal cord: 213.63166942864524
Size of spinal cord in z direction: 187.26147259119227
Ratio length/size: 1.1408201936712383
Safe zone boundaries (curved space): [-157.16939824714527, 30.092074344047006]
Safe zone boundaries (straight space): [-170.35449666587175, 43.2771727627735]
Pad input volume to account for spinal cord length…
Time to generate centerline: 26.0 ms
100%|█████████████████████████████████████████| 268/268 [00:08<00:00, 32.53it/s]
100%|█████████████████████████████████████████| 370/370 [00:57<00:00, 6.39it/s]
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image…
/Users/Akash/sct_4.2.2/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n ‘BSpline[3]’ # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.681805-straighten_spinalcord-392zp5eg
Generate output files…
File created: ./warp_curve2straight.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.681805-straighten_spinalcord-392zp5eg/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
sct_convert -i /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.681805-straighten_spinalcord-392zp5eg/tmp.anat_rigid_warp.nii.gz -o ./data_straight.nii
File created: ./data_straight.nii
Remove temporary files…
rm -rf /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.681805-straighten_spinalcord-392zp5eg
Finished! Elapsed time: 85 s
Done! To view results, type:
fslview_deprecated ./data_straight.nii &
Resample to 0.5mm isotropic…
sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b
Apply straightening to segmentation…
/Users/Akash/sct_4.2.2/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b
sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b
Create label to identify disc…
Creating temporary folder…
Run C2-C3 detector…
C2-C3 detected…
Remove temporary files…
rm -rf /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180220.405252-y9o_losx
WARNING: File /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b/labelz.nii.gz already exists. Will overwrite it.
Done! To view results, type:
fslview_deprecated /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b/labelz.nii.gz &
And apply straightening to label…
/Users/Akash/sct_4.2.2/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -r data_straightr.nii -t warp_curve2straight.nii.gz -o labelz_straight.nii.gz -n NearestNeighbor # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b
Get z and disc values from straight label…
… [327, 2]
Look for template…
Path template: /Users/Akash/sct_4.2.2/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: [962, 939, 908, 871, 834, 801, 770, 736, 693, 647, 601, 552, 501, 450, 397, 343, 290, 232, 169, 106, 56]
Distances between discs (in voxel): [23.0, 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, 63.0, 50.0]
Detect intervertebral discs…
Current disc: 2 (z=327). Direction: superior
… Peak found: z=-4 (correlation = 0.6317154456201127)
Current disc: 1 (z=354). Direction: superior
… correcting factor: 1.0
… Switching to inferior direction.
Current disc: 3 (z=290). Direction: inferior
… Peak found: z=-4 (correlation = 0.6053974905033584)
… correcting factor: 1.0
Current disc: 4 (z=249). Direction: inferior
… Peak found: z=4 (correlation = 0.516926118241018)
… correcting factor: 0.963963963963964
Current disc: 5 (z=221). Direction: inferior
… Peak found: z=1 (correlation = 0.5456549080765714)
… correcting factor: 0.9578214578214579
Current disc: 6 (z=192). Direction: inferior
… Peak found: z=1 (correlation = 0.5579264745007423)
… correcting factor: 0.9533539404507148
Current disc: 7 (z=161). Direction: inferior
… Peak found: z=1 (correlation = 0.5611317775204107)
… correcting factor: 0.9464224013559878
Current disc: 8 (z=121). Direction: inferior
… Peak found: z=5 (correlation = 0.6612274105215753)
… correcting factor: 0.9308205300659297
Current disc: 9 (z=83). Direction: inferior
… Peak found: z=1 (correlation = 0.6738742898572386)
… correcting factor: 0.9285983985902971
Current disc: 10 (z=41). Direction: inferior
… Peak found: z=2 (correlation = 0.5020518285435406)
… correcting factor: 0.9244546151720515
Adding top disc based on adjusted template distance: #0
… approximate distance: 21
Un-straighten labeling…
/Users/Akash/sct_4.2.2/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -r segmentation.nii -t warp_straight2curve.nii.gz -o segmentation_labeled.nii -n NearestNeighbor # in /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b
Clean labeled segmentation (correct interpolation errors)…
WARNING: File /private/var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b/segmentation_labeled.nii already exists. Will overwrite it.
Label discs…
Generate output files…
sct_convert -i /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b/segmentation_labeled.nii -o ./3D-T2W-S_seg_labeled.nii.gz
File created: ./3D-T2W-S_seg_labeled.nii.gz
sct_convert -i /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b/segmentation_labeled_disc.nii -o ./3D-T2W-S_seg_labeled_discs.nii.gz
File created: ./3D-T2W-S_seg_labeled_discs.nii.gz
File created: ./warp_curve2straight.nii.gz
File created: ./warp_straight2curve.nii.gz
File created: ./straight_ref.nii.gz
Remove temporary files…
rm -rf /var/folders/sw/ydq661bj3qxbnqcq33jpqpj40000gn/T/sct-20200519180049.342835-label_vertebrae-5nmo1e0b
*** Generate Quality Control (QC) html report ***
Resample images to NonexNone mm
QcImage: layout with Sagittal slice
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/css
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/css
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/css
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/css
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/css/style.css /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/css
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/css
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/js
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/js
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/js
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/js/main.js /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/js
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/js
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/js/animation.js /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/js
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/imgs
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/imgs
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/imgs
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/fonts
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/fonts
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/fonts
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/fonts
cp /Users/Akash/sct_4.2.2/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_assets/fonts
Successfully generated the QC results in /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/_json/qc_2020_05_19_180232.606575.json
Use the following command to see the results in a browser:
open “/Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/qc/index.html”
Done! To view results, type:
fslview_deprecated /Users/Akash/CanProCo/Cache/NIFTI/Edmonton/CAN-05-PPM-034-M0/SPINE/3D-T2W-S/3D-T2W-S.nii.gz -t 1 ./3D-T2W-S_seg_labeled.nii.gz -l MGH-Subcortical -t 0.5 &
This was successful when run in terminal using the syntax you provided. Also, sct_check_dependencies was all OK.
Not sure why sct_label_vertebrae is not working when I run my original script in Matlab.
Thanks for your help!
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