Update spinal levels based on Frostell et al. paper

[jcohenadad]

This PR updates the spinal levels with an improved version. See full context in #16.

 Generated with: d854c268d445fa5ed18b8928b730fd0a7c108c3a

As the new spinal levels are integer (vs. the previous spinal levels which were probabilistic), they are contained within a single file located under PAM50/template (previously PAM50/spinal_levels). The following changes are therefore necessary:

• [x] On the PAM50 side, fix the spinal cord segmentation #19
• [x] Generate PAM50_spinal_levels.nii.gz under PAM50/template
• [x] Start a discussion on the forum to get feedback from researchers about this plan
• [x] Remove PAM50/spinal_levels
• [x] On the SCT side: when running sct_warp_template, remove the option -s because the spinal levels will be warped by default alongside all files under PAM50/template
• [x] Regenerate 14 (point-labels) from the new full-cord level labels file
• [x] Add correct entry (15) in info_label.txt
• [x] https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4247
  • PR: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4249
• [x] https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4248
  • [ ] Unresolved course comment

Fixes #16

Related: https://github.com/spinalcordtoolbox/PAM50/pull/21

[jcohenadad]

As per https://github.com/spinalcordtoolbox/PAM50/issues/28#issuecomment-1771540105, a suggestion would be to have:

• one file for spinal level labels (one pixel per level): 14, point-wise spinal level labels, PAM50_label_spinal_levels.nii.gz
• one file for spinal levels (labeled segmentation): 15, spinal cord mask with spinal levels, PAM50_spinal_levels.nii.gz

[jcohenadad]

Oops! on 38f6ce3418aebcee1458594f22646dc94ca889f6 I noticed a value=1 at the very bottom:

It extends for 9 slices. Probably related to the code, which rounds segment length and then accumulate errors going caudally: https://github.com/spinalcordtoolbox/PAM50/blob/38f6ce3418aebcee1458594f22646dc94ca889f6/scripts/generate_spinal_levels.py#L94

[jcohenadad]

We can merge and fix https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4248 afterwards