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Create code to linearly register SC lesion masks in subject PSIR to subject MT space and calculate MTR for ROIs excluding SC lesions #91

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jcohenadad opened this issue May 14, 2024 · 6 comments · May be fixed by #95
Open

Create code to linearly register SC lesion masks in subject PSIR to subject MT space and calculate MTR for ROIs excluding SC lesions #91

jcohenadad opened this issue May 14, 2024 · 6 comments · May be fixed by #95

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@jcohenadad
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This issue is a followup from #88 (comment). After merging #90 we want to modify @leelisae's code to add the following features:

  • linearly register SC lesion masks in subject PSIR to subject MT space
  • calculate MTR for ROIs excluding SC lesions
@jcohenadad jcohenadad mentioned this issue May 14, 2024
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@jcohenadad
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@leelisae I'm using the data you sent me on 2024-05-15, but I neither see the PSIR image, nor the lesion segmentation. See for example the files for one subject:

julien-macbook:~/Desktop/canproco/data/CAN-01-RRM-133-M0 $ tree
.
├── mt
│   ├── mt0.nii.gz
│   ├── mt1.nii.gz
│   └── mt_t1.nii.gz
└── t2
    └── t2.nii.gz

Wasn't the plan that you run @plbenveniste's model to get the lesion segmentation as per our discussion #88? Once you do it, you can send me the data that include the lesion segmentation, so I can work on the registration and metric extraction code. Given that the lesion masks are derivatives, I suggest you add them in your dataset as an extra folder 'derivatives'.

@jcohenadad jcohenadad mentioned this issue May 16, 2024
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@leelisae
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@jcohenadad - I understood that once we confirmed that there were no issues with the BIDS ID numbers within each site (#88), I can use the lesion masks that your team has already generated instead of having to redo the processing again. If I’m correct in my understanding, I have received the lesion masks and I’ve added both the lesion mask and the PSIR image to the data folder in our shared Dropbox.

I’m not sure if I understood the part re: “derivatives” folder. I added this folder as I understood, but if I’m misunderstood, please feel free to relocate it appropriately, and I will follow your instructions when analyzing non-lesional MTR of the SC using the lesion masks generated from the PSIR sequence for the rest of the subjects later.

I also found it interesting that lesion masks were generated for healthy controls, as shown in the example in Dropbox. Do you believe that the lesion masks are accurate for healthy controls, or would it be more reasonable to process non-lesional MTR in the SC for patients only?

Thank you for all your help! I'm excited to learn which command lines are optimal to use for the features you listed above.

@jcohenadad
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Good, the example dataset version 2024-05-16_14h55min (@leelisae please always refer to the date/time of the dataset, to make sure we both refer to the same dataset when going back-and-forth with analysis debugging/interpretation) seems to have the PSIR and lesion masks:

.
├── CAN-01-CON-039-M0
│   ├── mt
│   │   ├── mt0.nii.gz
│   │   ├── mt1.nii.gz
│   │   └── mt_t1.nii.gz
│   ├── psir
│   │   └── psir.nii.gz
│   └── t2
│       └── t2.nii.gz
├── CAN-01-RRM-133-M0
│   ├── mt
│   │   ├── mt0.nii.gz
│   │   ├── mt1.nii.gz
│   │   └── mt_t1.nii.gz
│   ├── psir
│   │   └── psir.nii.gz
│   └── t2
│       └── t2.nii.gz
├── CAN-03-RRM-092-M0
│   ├── mt
│   │   ├── mt0.nii.gz
│   │   ├── mt1.nii.gz
│   │   └── mt_t1.nii.gz
│   ├── psir
│   │   └── psir.nii.gz
│   └── t2
│       └── t2.nii.gz
├── derivatives
│   └── lesion_masks
│       ├── CAN-01-CON-039-M0_lesion.nii.gz
│       ├── CAN-01-RRM-133-M0_lesion.nii.gz
│       └── CAN-03-RRM-092-M0_lesion.nii.gz
└── qc

I should be able to move forward with the analysis code.

I understood that once we confirmed that there were no issues with the BIDS ID numbers within each site (#88), I can use the lesion masks that your team has already generated instead of having to redo the processing again. If I’m correct in my understanding, I have received the lesion masks and I’ve added both the lesion mask and the PSIR image to the data folder in our shared Dropbox.

Yes, this is exactly it!

I’m not sure if I understood the part re: “derivatives” folder. I added this folder as I understood, but if I’m misunderstood, please feel free to relocate it appropriately, and I will follow your instructions when analyzing non-lesional MTR of the SC using the lesion masks generated from the PSIR sequence for the rest of the subjects later.

The derivatives folder is a BIDS requirement, and is a way to ensure reproducible pipeline (also see #92). The derivatives folder you produced does not completely follow BIDS convention, but since I understand you are pressed with time, this will be good enough for now.

I also found it interesting that lesion masks were generated for healthy controls, as shown in the example in Dropbox. Do you believe that the lesion masks are accurate for healthy controls, or would it be more reasonable to process non-lesional MTR in the SC for patients only?

That's an issue with the model, which is not perfect (no model is perfect). Tagging @plbenveniste

@jcohenadad
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Testing lisa/spine.sh version 8f7fbdb on data version 2024-05-16_14h55min, on subject CAN-01-RRM-133-M0, I encountered some errors:

Terminal output 
julien-macbook:~/Desktop/canproco $ sh ~/code/canproco/lisa/spine.sh data/CAN-01-RRM-133-M0 qc
data/CAN-01-RRM-133-M0: spine.sh started at 21/05/2024_03:03:53 pm

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_image -i t2.nii.gz -setorient RPI -o t2.nii.gz
--

/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/t2.nii.gz
Generate output files...
File t2.nii.gz already exists. Will overwrite it.

Done! To view results, type:
fsleyes t2.nii.gz &


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

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

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t2
  Threshold: 0.7
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-03-58_deepseg-sc_mqqqikyl)
Reorient the image to RPI, if necessary...
Converting image from type 'int16' to type 'float64' for linear interpolation
Finding the spinal cord centerline...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-01_optic-detect-centerline_sg6yc5va)
Remove temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-01_optic-detect-centerline_sg6yc5va
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 #223
Image header specifies datatype 'float32', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'.
Converting image from type 'uint8' to type 'float64' for linear interpolation
Compute shape analysis: 100%|██████████████| 224/224 [00:00<00:00, 252.16iter/s]
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-03-58_deepseg-sc_mqqqikyl

*** Generate Quality Control (QC) html report ***
Resampling image "t2.nii.gz" to 0.6x0.6 mm
Converting image from type 'int16' to type 'float64' for spline interpolation
Resampling image "t2_seg.nii.gz" to 0.6x0.6 mm
Converting image from type 'uint8' to type 'float64' for linear interpolation
Image header specifies datatype 'float64', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
QcImage: layout with Axial slice
Compute center of mass at each slice
/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/scipy/ndimage/_measurements.py:1542: RuntimeWarning: invalid value encountered in scalar divide
  results = [sum(input * grids[dir].astype(float), labels, index) / normalizer
/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/data/CAN-01-RRM-133-M0/t2/sct_deepseg_sc/2024_05_21_150423.083541/background_img.png
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/css
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/css
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/css
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/css/style.css /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/css
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/filesaver.min.js /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/js
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/js
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/js
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/main.js /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/js
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/js
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/js/yaml.min.js /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/js
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/f-icon.png /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/imgs
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyright.png /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/imgs
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keydown.png /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/imgs
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/keyup.png /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/imgs
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/imgs
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/fonts
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/fonts
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/fonts
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/fonts
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/fonts
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/html/index.html /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/html
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/py/__init__.py /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/py
cp /Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/reports/assets/_assets/py/refresh_qc_entries.py /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_assets/py
Successfully generated the QC results in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_json/qc_2024_05_21_150423.083541.json

To see the results in a browser, type:
open /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/index.html


Done! To view results, type:
fsleyes t2.nii.gz -cm greyscale t2_seg.nii.gz -cm red -a 70.0 &


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc qc
--

Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz)

Copying input data to tmp folder...

Straighten spinal cord...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_straighten-spinalcord_4iphg1of)
Copy files to tmp folder...
Fitting centerline using B-spline approximation
Error on approximation = 2.13 mm
Error on approximation = 0.34 mm
Error on approximation = 0.4 mm
Error on approximation = 0.24 mm
Error on approximation = 0.15 mm
Error on approximation = 0.16 mm
Error on approximation = 0.14 mm
Error on approximation = 0.13 mm
Error on approximation = 0.12 mm
Error on approximation = 0.11 mm
Error on approximation = 0.1 mm
Error on approximation = 0.1 mm
Create the straight space and the safe zone
Length of spinal cord: 183.93273777310836
Size of spinal cord in z direction: 175.7116825840148
Ratio length/size: 1.046787186077754
Safe zone boundaries (curved space): [-248.41161818807487, -72.69993560406007]
Safe zone boundaries (straight space): [-252.52214578262164, -68.58940800951329]
Pad input volume to account for spinal cord length...
Time to generate centerline: 17.0 ms
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 228/228 [00:03<00:00, 59.96it/s]
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 336/336 [00:21<00:00, 15.62it/s]
Image header specifies datatype 'float32', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Warping field generated: tmp.curve2straight.nii.gz
Image header specifies datatype 'float32', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_straighten-spinalcord_4iphg1of
Generate output files...
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_straighten-spinalcord_4iphg1of/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_straighten-spinalcord_4iphg1of/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_straighten-spinalcord_4iphg1of/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
File created: ./data_straight.nii
Remove temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_straighten-spinalcord_4iphg1of

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

Apply straightening to segmentation...
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz
File /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz/segmentation_straight.nii already exists. Will overwrite it.

Create label to identify disc...
Creating temporary folder...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-04_detect-c2c3_l0u8obag)
Run C2-C3 detector...
C2-C3 detected...
Remove temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-04_detect-c2c3_l0u8obag
File /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz/labelz.nii.gz already exists. Will overwrite it.

And apply straightening to label...
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz

Get z and disc values from straight label...
.. [300, 3]
Look for template...
Path template: /Users/julien/code/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: [984, 938, 907, 870, 833, 800, 769, 735, 692, 646, 600, 551, 500, 449, 396, 342, 289, 231, 168, 105, 39]
Distances between discs (in voxel): [46.0, 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, 66.0]
Detect intervertebral discs...
Current disc: 2 (z=300). Direction: superior
.. Peak found: z=-4 (correlation = 0.38128107973592007)
Current disc: 1 (z=327). Direction: superior
.. correcting factor: 1.0
.. Switching to inferior direction.
Current disc: 3 (z=263). Direction: inferior
.. Peak found: z=1 (correlation = 0.4843182741664749)
.. correcting factor: 0.9324324324324325
Current disc: 4 (z=230). Direction: inferior
.. Peak found: z=-4 (correlation = 0.4828105797896957)
.. correcting factor: 0.963963963963964
Current disc: 5 (z=194). Direction: inferior
.. Peak found: z=-1 (correlation = 0.4628382734736265)
.. correcting factor: 0.972972972972973
Current disc: 6 (z=163). Direction: inferior
.. Peak found: z=-3 (correlation = 0.517582305620323)
.. correcting factor: 0.99128160418483
Current disc: 7 (z=126). Direction: inferior
.. Peak found: z=3 (correlation = 0.47165516401294705)
.. correcting factor: 0.9780287878010839
Current disc: 8 (z=87). Direction: inferior
.. Peak found: z=1 (correlation = 0.3974775151997078)
.. correcting factor: 0.9745230141285038
Current disc: 9 (z=43). Direction: inferior
.. Peak found: z=5 (correlation = 0.3856986960305723)
.. correcting factor: 0.9614032895363538
Current disc: 10 (z=4). Direction: inferior
.. Peak found: z=9 (correlation = 0.39838124385098395)
.. correcting factor: 0.9391217646120246
Adding top disc based on adjusted template distance: #0
.. approximate distance: 43

Un-straighten labeling...
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz

Cleaning labeled segmentation:
  removing labeled voxels outside segmentation...
Done cleaning.
File /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz/segmentation_labeled.nii already exists. Will overwrite it.

Label discs...

Un-straighten labeled discs...

Dilate labels before warping...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-12_apply-transfo-3d-label_6ue49hjl)
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-12_apply-transfo-3d-label_6ue49hjl/dilated_data.nii -o segmentation_labeled_disc.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz

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: /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/t2_seg_labeled.nii.gz
File created: /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/t2_seg_labeled_discs.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz/straightening.cache /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/straightening.cache
File created: /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/straightening.cache
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz/warp_curve2straight.nii.gz /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/warp_curve2straight.nii.gz
File created: /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/warp_curve2straight.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz/warp_straight2curve.nii.gz /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/warp_straight2curve.nii.gz
File created: /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/warp_straight2curve.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz/straight_ref.nii.gz /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/straight_ref.nii.gz
File created: /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/straight_ref.nii.gz

Remove temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-04-26_label-vertebrae_6b323rzz

*** Generate Quality Control (QC) html report ***
QcImage: layout with Sagittal slice
/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/data/CAN-01-RRM-133-M0/t2/sct_label_vertebrae/2024_05_21_150517.308802/background_img.png
Successfully generated the QC results in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_json/qc_2024_05_21_150517.308802.json

To see the results in a browser, type:
open /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/index.html


Done! To view results, type:
fsleyes t2.nii.gz -cm greyscale -a 100.0 t2_seg_labeled.nii.gz -cm subcortical -a 50.0 &


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 3,5 -o t2_labels_vert.nii.gz
--

Generating output files...

Done! To view results, type:
fsleyes t2_seg_labeled.nii.gz t2_labels_vert.nii.gz &


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_qc -i t2.nii.gz -s t2_labels_vert.nii.gz -p sct_label_utils -qc qc
--


*** Generate Quality Control (QC) html report ***
QcImage: layout with Sagittal slice
qc/data/CAN-01-RRM-133-M0/t2/sct_label_utils/2024_05_21_150521.312335/background_img.png
Successfully generated the QC results in qc/_json/qc_2024_05_21_150521.312335.json

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


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_vert.nii.gz -c t2 -qc qc
--


Check template files...
  OK: /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz
  OK: /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz
  OK: /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz

Check parameters:
  Data:                 t2.nii.gz
  Landmarks:            t2_labels_vert.nii.gz
  Segmentation:         t2_seg.nii.gz
  Path template:        /Users/julien/code/spinalcordtoolbox/data/PAM50
  Remove temp files:    1

Check input labels...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox)

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

Change orientation of input images to RPI...

Resample data to 1mm isotropic...
load data...
Converting image from type 'int16' to type 'float64' for linear interpolation

Done! To view results, type:
fsleyes data_rpi_1mm.nii &

load data...
Converting image from type 'uint8' to type 'float64' for linear interpolation

Done! To view results, type:
fsleyes seg_bin_rpi_1mm.nii.gz &

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

Straighten the spinal cord using centerline/segmentation...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y)
Copy files to tmp folder...
File /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y/centerline_rpi.nii.gz already exists. Will overwrite it.
Create the straight space and the safe zone
Length of spinal cord: 184.4883691140574
Size of spinal cord in z direction: 176.1772127122498
Ratio length/size: 1.047174979521229
Safe zone boundaries (curved space): [-248.45713558582204, -72.27992287357225]
Safe zone boundaries (straight space): [-252.61271378672586, -68.12434467266844]
Pad input volume to account for spinal cord length...
Time to generate centerline: 16.0 ms
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 184/184 [00:03<00:00, 49.20it/s]
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 194/194 [00:07<00:00, 25.30it/s]
Image header specifies datatype 'float32', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Warping field generated: tmp.curve2straight.nii.gz
Image header specifies datatype 'float32', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y
Generate output files...
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz
File created: ./warp_curve2straight.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y/tmp.anat_rigid_warp.nii.gz /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/seg_bin_rpi_1mm_crop_straight.nii.gz
File created: /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/seg_bin_rpi_1mm_crop_straight.nii.gz
Remove temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-31_straighten-spinalcord_27lpij7y
/Users/julien/code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/data_rpi_1mm.nii warp_straight2curve.nii.gz # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox

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...
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/label_projected_rpi_1mm_dilate.nii.gz -o /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/label_projected_rpi_1mm_dilate_straight.nii.gz -t warp_curve2straight.nii.gz -r /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/seg_bin_rpi_1mm_crop_straight.nii.gz -n NearestNeighbor # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox

Estimate transformation for step #0...
Labels src: [[-12.989009665255331, 21.020957333508886, -115.7399487443337], [-18.32404148351408, 20.708072310129904, -151.1567461340793]]
Labels dest: [[-0.0, 45.720001220703125, -117.34002685546875], [-0.0, 45.720001220703125, -153.34002685546875]]
Degrees of freedom (dof): Tx_Ty_Tz_Sz
Optimization terminated successfully.
         Current function value: 14.280231
         Iterations: 2
         Function evaluations: 186
Matrix:
 [[ 1.  0.  0.]
 [ 0.  1.  0.]
 [-0.  0.  1.]]
Center:
 [   0.           45.72000122 -135.34002686]
Translation:
 [[-15.65652557 -24.85548639   1.89167943]]

Concatenate transformations: curve --> straight --> affine...
/Users/julien/code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_curve2straightAffine.nii.gz -R template.nii straight2templateAffine.txt warp_curve2straight.nii.gz # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox

Apply transformation...
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/data_rpi_1mm.nii -o /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/data_rpi_1mm_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n 'BSpline[3]' # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/seg_bin_rpi_1mm_crop.nii.gz -o /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/seg_bin_rpi_1mm_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox
Image header specifies datatype 'float64', but array is of type '<class 'numpy.uint8'>'. Header metadata will be overwritten to use '<class 'numpy.uint8'>'.

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

Sub-sample in z-direction (for faster processing)...
load data...
Converting image from type 'uint16' to type 'float64' for linear interpolation
load data...
Converting image from type 'uint8' to type 'float64' for linear interpolation
load data...
load data...

Register straight spinal cord to template...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg)

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 (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-10_register-slicewise__qc1qbf_)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 141 x 141 x 92
  voxel size: 0.5mm x 0.5mm x 92mm

Split input segmentation...

Split destination segmentation...

Split input image...

Split destination image...

Estimate cord angle for each slice:   0%|                                  | 0/92 [00:00<?, ?iter/s]Switched to method 'hog' for slice: 0
Switched to method 'hog' for slice: 4
Estimate cord angle for each slice:  97%|████████████████████████▏| 89/92 [00:01<00:00, 50.41iter/s]Switched to method 'hog' for slice: 91
Estimate cord angle for each slice: 100%|█████████████████████████| 92/92 [00:01<00:00, 50.02iter/s]
Build 3D deformation field: 100%|█████████████████████████████████| 92/92 [00:05<00:00, 16.27iter/s]

Generate warping field...
Image header specifies datatype 'float32', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
 --> step1Warp.nii.gz

Generate warping field...
Image header specifies datatype 'float32', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
 --> step1InverseWarp.nii.gz

Move warping fields...
cp step1Warp.nii.gz /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg
cp step1InverseWarp.nii.gz /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-10_register-slicewise__qc1qbf_

--
ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg
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
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg

Concatenate transformations...
/Users/julien/code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg
/Users/julien/code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg

Apply transfo source --> dest...
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg

Apply transfo dest --> source...
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg

Generate output files...
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg/src_reg.nii data_rpi_1mm_straightAffine_crop_sub_reg.nii
File created: data_rpi_1mm_straightAffine_crop_sub_reg.nii
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg/warp_src2dest.nii.gz warp_data_rpi_1mm_straightAffine_crop_sub2template_crop_sub.nii.gz
File created: warp_data_rpi_1mm_straightAffine_crop_sub2template_crop_sub.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg/dest_reg.nii template_crop_sub_reg.nii
File created: template_crop_sub_reg.nii
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg/warp_dest2src.nii.gz warp_template_crop_sub2data_rpi_1mm_straightAffine_crop_sub.nii.gz
File created: warp_template_crop_sub2data_rpi_1mm_straightAffine_crop_sub.nii.gz

Remove temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-06-09_register-wrapper_1uwvzwfg

Concatenate transformations: anat --> template...
/Users/julien/code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_anat2template.nii.gz -R template.nii warp_data_rpi_1mm_straightAffine_crop_sub2template_crop_sub.nii.gz warp_curve2straightAffine.nii.gz # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox

Concatenate transformations: template --> anat...
/Users/julien/code/spinalcordtoolbox/bin/isct_ComposeMultiTransform 3 warp_template2anat.nii.gz -R data.nii warp_straight2curve.nii.gz -i straight2templateAffine.txt warp_template_crop_sub2data_rpi_1mm_straightAffine_crop_sub.nii.gz # in /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox
/Users/julien/code/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 /private/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox

Generate output files...
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/warp_template2anat.nii.gz warp_template2anat.nii.gz
File created: warp_template2anat.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/warp_anat2template.nii.gz warp_anat2template.nii.gz
File created: warp_anat2template.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/template2anat.nii.gz template2anat.nii.gz
File created: template2anat.nii.gz
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/anat2template.nii.gz anat2template.nii.gz
File created: anat2template.nii.gz
File straightening.cache already exists. Deleting it..
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/straightening.cache straightening.cache
File created: straightening.cache
File warp_curve2straight.nii.gz already exists. Deleting it..
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
File created: warp_curve2straight.nii.gz
File warp_straight2curve.nii.gz already exists. Deleting it..
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
File created: warp_straight2curve.nii.gz
File straight_ref.nii.gz already exists. Deleting it..
mv /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox/straight_ref.nii.gz straight_ref.nii.gz
File created: straight_ref.nii.gz

Delete temporary files...
rm -rf /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-05-25_register-to-template_iqlil2ox

Finished! Elapsed time: 118s

*** Generate Quality Control (QC) html report ***
Resampling image "t2.nii.gz" to 0.6x0.6 mm
Converting image from type 'int16' to type 'float64' for spline interpolation
Resampling image "template2anat.nii.gz" to 0.6x0.6 mm
Resampling image "t2_seg.nii.gz" to 0.6x0.6 mm
Converting image from type 'uint8' to type 'float64' for linear interpolation
Image header specifies datatype 'float64', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
QcImage: layout with Axial slice
Compute center of mass at each slice
/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/scipy/ndimage/_measurements.py:1542: RuntimeWarning: invalid value encountered in scalar divide
  results = [sum(input * grids[dir].astype(float), labels, index) / normalizer
/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/data/CAN-01-RRM-133-M0/t2/sct_register_to_template/2024_05_21_150729.684801/background_img.png
Successfully generated the QC results in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_json/qc_2024_05_21_150729.684801.json

To see the results in a browser, type:
open /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/index.html


Done! To view results, type:
fsleyes t2.nii.gz template2anat.nii.gz &


Done! To view results, type:
fsleyes /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz &


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

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


Check parameters:
  Working directory ........ /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
  Destination image ........ t2.nii.gz
  Warping field ............ warp_template2anat.nii.gz
  Path template ............ /Users/julien/code/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2

Dilate labels before warping...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-07-54_apply-transfo-3d-label_i6hptd97)
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-07-54_apply-transfo-3d-label_i6hptd97/dilated_data.nii -o label/template/PAM50_label_body.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2

Take the center of mass of each registered dilated labels...
File label/template/PAM50_label_body.nii.gz already exists. Will overwrite it.

Dilate labels before warping...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-08-05_apply-transfo-3d-label_rc4iqr2l)
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-08-05_apply-transfo-3d-label_rc4iqr2l/dilated_data.nii -o label/template/PAM50_label_disc.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2

Take the center of mass of each registered dilated labels...
File label/template/PAM50_label_disc.nii.gz already exists. Will overwrite it.

Dilate labels before warping...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-08-17_apply-transfo-3d-label_34m6xw19)
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-08-17_apply-transfo-3d-label_34m6xw19/dilated_data.nii -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2

Take the center of mass of each registered dilated labels...
File label/template/PAM50_label_discPosterior.nii.gz already exists. Will overwrite it.
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/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 /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2

Dilate labels before warping...
Creating temporary folder (/var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-08-31_apply-transfo-3d-label_6zj3ln9l)
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /var/folders/5f/6n99hhyj5_g5cv_1bbx1q7cr0000gn/T/sct_2024-05-21_15-08-31_apply-transfo-3d-label_6zj3ln9l/dilated_data.nii -o label/template/PAM50_spinal_midpoint.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2

Take the center of mass of each registered dilated labels...
File label/template/PAM50_spinal_midpoint.nii.gz already exists. Will overwrite it.
/Users/julien/code/spinalcordtoolbox/bin/isct_antsApplyTransforms -d 3 -i /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_spinal_levels.nii.gz -o label/template/PAM50_spinal_levels.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
cp /Users/julien/code/spinalcordtoolbox/data/PAM50/template/info_label.txt label/template

*** Generate Quality Control (QC) html report ***
Resampling image "t2.nii.gz" to 0.6x0.6 mm
Converting image from type 'int16' to type 'float64' for spline interpolation
Resampling image "PAM50_wm.nii.gz" to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/scipy/ndimage/_measurements.py:1542: RuntimeWarning: invalid value encountered in scalar divide
  results = [sum(input * grids[dir].astype(float), labels, index) / normalizer
/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/data/CAN-01-RRM-133-M0/t2/sct_warp_template/2024_05_21_150848.230939/background_img.png
Successfully generated the QC results in /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/_json/qc_2024_05_21_150848.230939.json

To see the results in a browser, type:
open /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/qc/index.html


Done! To view results, type:
fsleyes t2.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 red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_process_segmentation -i t2_seg.nii.gz -vert 2:4 -vertfile ./label/template/PAM50_levels.nii.gz -o csa_c2c4.csv -append 0
--

Converting image from type 'uint8' to type 'float64' for linear interpolation
Compute shape analysis: 100%|██████████████| 223/223 [00:00<00:00, 260.66iter/s]
Aggregating metrics: 100%|██████████████████████| 9/9 [00:02<00:00,  3.15iter/s]

Done! To view results, type:
open /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/csa_c2c4.csv

/Users/julien/code/canproco/lisa/spine.sh: line 54: cd: data/CAN-01-RRM-133-M0/mt: No such file or directory

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_image -i mt_t1.nii.gz -setorient RPI -o mt_t1.nii.gz
--

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 100, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt_t1.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_image.py", line 655, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_image.py", line 257, in main
    im_in_list = [Image(fname) for fname in fname_in]
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_image.py", line 257, in <listcomp>
    im_in_list = [Image(fname) for fname in fname_in]
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 285, in __init__
    raise e
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 280, in __init__
    self.loadFromPath(param, mmap, verbose)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 428, in loadFromPath
    im_file = nib.load(self.absolutepath, mmap=mmap)
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 102, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt_t1.nii.gz'

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_deepseg_sc -i mt_t1.nii.gz -c t1 -qc qc
--

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 100, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt_t1.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_deepseg_sc.py", line 211, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_deepseg_sc.py", line 182, in main
    check_dim(fname_image, dim_lst=[2, 3])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 1460, in check_dim
    dim = Image(fname).hdr['dim'][:4]
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 285, in __init__
    raise e
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 280, in __init__
    self.loadFromPath(param, mmap, verbose)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 428, in loadFromPath
    im_file = nib.load(self.absolutepath, mmap=mmap)
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 102, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt_t1.nii.gz'

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_create_mask -i mt_t1.nii.gz -p centerline,mt_t1_seg.nii.gz -size 35mm -f cylinder -o mt_t1_mask.nii.gz
--


ERROR: The file mt_t1_seg.nii.gz does not exist. Exit program.


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_register_multimodal -i /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz -iseg /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz -d mt_t1.nii.gz -dseg mt_t1_seg.nii.gz -m mt_t1_mask.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=syn,metric=CC,iter=5,gradStep=0.5 -initwarp data/CAN-01-RRM-133-M0/t2/warp_template2anat.nii.gz -initwarpinv data/CAN-01-RRM-133-M0/t2/warp_anat2template.nii.gz -owarp warp_template2mt.nii.gz -qc qc
--


Input parameters:
  Source .............. /Users/julien/code/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz (141, 141, 991)
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 100, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt_t1.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 443, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 376, in main
    printv(f'  Destination ......... {fname_dest} {Image(fname_dest).data.shape}')
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 285, in __init__
    raise e
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 280, in __init__
    self.loadFromPath(param, mmap, verbose)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 428, in loadFromPath
    im_file = nib.load(self.absolutepath, mmap=mmap)
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 102, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt_t1.nii.gz'

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_warp_template -d mt_t1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc qc
--


Check parameters:
  Working directory ........ /Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2
  Destination image ........ mt_t1.nii.gz
  Warping field ............ warp_template2mt.nii.gz
  Path template ............ /Users/julien/code/spinalcordtoolbox/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 100, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/warp_template2mt.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_warp_template.py", line 310, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_warp_template.py", line 274, in main
    w = WarpTemplate(fname_src, fname_transfo, warp_atlas, folder_out, path_template,
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_warp_template.py", line 71, in __init__
    warp_label(self.path_template, self.folder_template, self.file_info_label, self.fname_src,
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_warp_template.py", line 115, in warp_label
    sct_apply_transfo.main(['-i', fname_label,
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_apply_transfo.py", line 345, in main
    transform.apply()
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_apply_transfo.py", line 159, in apply
    and Image(list_warp[idx_warp]).header.get_intent()[0] != 'vector':
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 285, in __init__
    raise e
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 280, in __init__
    self.loadFromPath(param, mmap, verbose)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 428, in loadFromPath
    im_file = nib.load(self.absolutepath, mmap=mmap)
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 102, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/warp_template2mt.nii.gz'

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_register_multimodal -i mt0.nii.gz -d mt_t1.nii.gz -dseg mt_t1_seg.nii.gz -m mt_t1_mask.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -x spline -o mt0_reg.nii.gz -qc qc
--


Input parameters:
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 100, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt0.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 443, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 375, in main
    printv(f'  Source .............. {fname_src} {Image(fname_src).data.shape}')
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 285, in __init__
    raise e
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 280, in __init__
    self.loadFromPath(param, mmap, verbose)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 428, in loadFromPath
    im_file = nib.load(self.absolutepath, mmap=mmap)
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 102, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt0.nii.gz'

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_register_multimodal -i mt1.nii.gz -d mt_t1.nii.gz -dseg mt_t1_seg.nii.gz -m mt_t1_mask.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -x spline -o mt1_reg.nii.gz -qc qc
--


Input parameters:
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 100, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt1.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 443, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_multimodal.py", line 375, in main
    printv(f'  Source .............. {fname_src} {Image(fname_src).data.shape}')
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 285, in __init__
    raise e
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 280, in __init__
    self.loadFromPath(param, mmap, verbose)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 428, in loadFromPath
    im_file = nib.load(self.absolutepath, mmap=mmap)
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 102, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt1.nii.gz'

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1_reg.nii.gz
--


Compute MTR...
Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 100, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt1_reg.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_compute_mtr.py", line 89, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_compute_mtr.py", line 79, in main
    nii_mtr = compute_mtr(nii_mt1=Image(arguments.mt1), nii_mt0=Image(arguments.mt0), threshold_mtr=arguments.thr)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 285, in __init__
    raise e
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 280, in __init__
    self.loadFromPath(param, mmap, verbose)
  File "/Users/julien/code/spinalcordtoolbox/spinalcordtoolbox/image.py", line 428, in loadFromPath
    im_file = nib.load(self.absolutepath, mmap=mmap)
  File "/Users/julien/code/spinalcordtoolbox/python/envs/venv_sct/lib/python3.9/site-packages/nibabel/loadsave.py", line 102, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt1_reg.nii.gz'

--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 50 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_cord.csv -append 0
--


ERROR: mtr.nii.gz does not exist. Exit program.


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 52 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_gm.csv -append 0
--


ERROR: mtr.nii.gz does not exist. Exit program.


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 51 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_wm.csv -append 0
--


ERROR: mtr.nii.gz does not exist. Exit program.


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 53 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_dc.csv -append 0
--


ERROR: mtr.nii.gz does not exist. Exit program.


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 54 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_lf.csv -append 0
--


ERROR: mtr.nii.gz does not exist. Exit program.


--
Spinal Cord Toolbox (git-master-e5525085b7d8531416a7fee304d8a71714d540ba)

sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 55 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -z 3:18 -o csv/mtr_vf.csv -append 0
--


ERROR: mtr.nii.gz does not exist. Exit program.

data/CAN-01-RRM-133-M0: spine.sh finished at 21/05/2024_03:09:20 pm
data/CAN-01-RRM-133-M0: spine.sh duration: 327 seconds

The first error is:

FileNotFoundError: No such file or no access: '/Users/julien/Desktop/canproco/data/CAN-01-RRM-133-M0/t2/mt_t1.nii.gz'

Apparently the code is expecting a file t2/mt_t1.nii.gz, but this file is under mt/ and not under t2/. @leelisae it seems that either the data or the code you sent me is faulty. Please send me a working version, so I can start implementing the requested feature.

@lisaeylee
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@jcohenadad - This is strange. I tested lisa/spine.sh using SCT 5.7 on data version 2024-05-16_14h55min, on subject CAN-01-RRM-133-M0 and CAN-03-RRM-092-M0, and did not encounter any errors and generated all expected QCs too.

There is a line cd ${SUBJECT}/mt prior to performing sct_image -i mt_t1.nii.gz -setorient RPI -o mt_t1.nii.gz; so the code should know to change to the correct directory mt/ for mt/mt_t1.nii.gz. I will add a ";" at the end of cd ${SUBJECT}/mt but I don't think this is the issue as I was able to run the script without this.

Terminal Saved Output.pdf

@jcohenadad jcohenadad mentioned this issue May 23, 2024
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@jcohenadad
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jcohenadad commented May 23, 2024 •
edited
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Cause of the issue reported in #91 (comment) is now explained in #93

After fixing #93 the script is running properly! I was able to fully process a subject 😊.

@jcohenadad jcohenadad linked a pull request May 23, 2024 that will close this issue
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This was referenced May 27, 2024
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Implemented method to register lesion mask to MT space ivadomed/canproco
3 participants
@jcohenadad @leelisae @lisaeylee