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Updated PAM50 cord mask #49

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Updated PAM50 cord mask #49

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@jcohenadad jcohenadad commented Sep 8, 2025 •
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The current cord segmentation is too small and not representative of the spinal cord CSA (see notably discussions with @vcallot).

This PR re-generates the PAM50 cord mask using the following steps:

  • re-create the PAM50_cord mask using the contrast-agnostic model
  • symmetrize the output

Below is the comparison between the current (red) and the new (green) cord mask:

Screen.Recording.2025-09-08.at.15.32.50.mov

Fixes #48

@jcohenadad jcohenadad changed the title Added script to generate cord mask Updated PAM50 cord mask Sep 8, 2025
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Maybe some slices don't look realistic:

image

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vcallot commented Sep 10, 2025

@jcohenadad and the team, thanks a lot for all the efforts and hard work!

With regard to the new PAM50_cord mask (green), it looks undoubtedly better.
Two remarks though :

  1. at the thoracic level, especially T1 to T9, common pixels are not visible on the video -> could you check that the green mask is not smaller than the red one, especially in the R-L direction. If smaller, it may be better to keep the union of both red and green masks.
  2. at the lumbar level L1, I agree with the comment above from Julien, the mask is not too realistic and previous version (red one) better matched what remains of the cord. I would not be too confident in quantification at this level but since some groups may be interested, it would be better to be on the safe side and only include soft tissues and no nerve roots. Can this be manually corrected ?

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@vcallot Thank you for your feedback. About (1): I regenerated a screen recording, adjusting the opacity so we can better appreciate the older vs. the newer mask. The new recording also focuses on the thoracic level.

I do agree that, for some slices (not the majority though), the older cord mask is RL wider that the newer mask. However, when looking at the actual T2w image, I still find that the newer cord mask is more truthful to the actual cord boundary, therefore I would advise against performing the union of both the older and newer masks.

Screen.Recording.2025-09-10.at.08.46.43.mov

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@vcallot:

at the lumbar level L1, I agree with the comment above from Julien, the mask is not too realistic and previous version (red one) better matched what remains of the cord. I would not be too confident in quantification at this level but since some groups may be interested, it would be better to be on the safe side and only include soft tissues and no nerve roots. Can this be manually corrected ?

Yes, it can be manually corrected. But I will proceed programatically (ie: labels edited in the script that generates the updated cord mask) for better reproducibility.

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jcohenadad commented Sep 11, 2025 •
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Given that the older version of the PAM50_cord is better towards the lumbo-sacral cord, I decided to keep it for that section, and to replace the section above it. A good z to define the beginning of that section is z=105, because this is where the two masks (old and new) have almost the same CSA:

To do this programatically, here is the code to extract labels from the old mask:

# zero the mask above z=105 (do not crop, just zero)
sct_crop_image -i PAM50_cord_old.nii.gz -zmin 0 -zmax 105 -b 0 -o PAM50_cord_old_masked.nii.gz
# Extract label coordinates and values
sct_label_utils -i PAM50_cord_old_masked.nii.gz -display
Cord labels between z=0 and z=105 
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And here is the code to replace labels in the new cord mask:

# Mask cord below z=104
sct_crop_image -i PAM50_cord.nii.gz -zmin 104 -zmax -1 -b 0 -o PAM50_cord_masked.nii.gz
# Create labels at z=105 and below
sct_label_utils -i PAM50_cord_masked.nii.gz -o PAM50_cord_masked_new.nii.gz -create-add 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And here is the result (red: old | green: new | kaki: union):

Screen.Recording.2025-09-11.at.16.06.43.mov

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jcohenadad commented Sep 11, 2025 •
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Given that the older mask was recognized to have a slight under-segmentation (by almost one voxel), I've dilated the lower portion before adding it to the new mask. Here is the full code:

# zero the mask above z=105 (do not crop, just zero)
sct_crop_image -i PAM50_cord_old.nii.gz -zmin 0 -zmax 105 -b 0 -o PAM50_cord_old_masked.nii.gz
# Dilate cropped mask. Note: we perform a 3D dilation with a ball kernel instead of a 2D, in order to obtain a smaller dilation.
sct_maths -i PAM50_cord_old_masked.nii.gz -dil 1 -o PAM50_cord_old_masked_dil.nii.gz
# Extract label coordinates and values
sct_label_utils -i PAM50_cord_old_masked.nii.gz -display
Cord labels 
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Replace new mask with dilated lower section:

# Mask cord below z=104
sct_crop_image -i PAM50_cord.nii.gz -zmin 104 -zmax -1 -b 0 -o PAM50_cord_masked.nii.gz
# Create labels at z=105 and below
sct_label_utils -i PAM50_cord_masked.nii.gz -o PAM50_cord_masked_new.nii.gz -create-add 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And here is the result (red: old | green: new | kaki: union):

Screen.Recording.2025-09-11.at.16.27.10.mov

Looks pretty good to me. What do you think @vcallot ?

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vcallot commented Sep 12, 2025

The. mask around z=145/148 is a bit weird (the cord is not ovale anymore, but more like a bean, so there may be some CSF and nerve roots at these levels, but everything is clearly improved other than that! Great job @jcohenadad and SCT team, and thank you for the traceability .

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The. mask around z=145/148 is a bit weird (the cord is not ovale anymore, but more like a bean, so there may be some CSF and nerve roots at these levels

Agreed-- It shouldn't take me too much time to fix, so I'll fix it

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jcohenadad commented Sep 18, 2025 •
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I manually edited the 'bean-like' voxels, yielding this new mask (in green, vs. red for the previous version):

Screen.Recording.2025-09-18.at.16.21.42.mov

I'm uploading the edited mask here for reference: PAM50_cord_masked_new_copy.nii.gz

And the previous version: PAM50_cord_masked_new.nii.gz

Next step: identify pointwise labels below z=185 (where old and new differ) and replace mask with labels after cropping.

@stoeffels stoeffels mentioned this pull request Sep 19, 2025
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Before merging this PR we need to agree on the location of the lower tip of spinal cord #51

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Update cord segmentation based on contrast-agnostic model

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@jcohenadad @vcallot