spinalcordtoolbox / PAM50

https://github.com/neuropoly/spinalcordtoolbox
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Add cauda equinea label (`60`) to all three point label files for easier lumbar registration #27

Closed joshuacwnewton closed 11 months ago

joshuacwnewton commented 11 months ago

These changes will enable lumbar registration by adding a new cauda equinea label (60) to each of the three currently-used label files, to be used as an inferior landmark during registration.

Each of these files corresponds to one of three sct_register_to_template options (-l, -ldisc, -lspinal).

NOTE: Currently, this change will not actually work for the body labels (-l option), because of https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4229#issuecomment-1747234925. Right now, the body labels are programmatically generated from the spinal level file, and PAM50_label_body.nii.gz is completely ignored.

The label was added using FSLeyes:

(Side note: The file size increase is quite dramatic for 2 of the 3 files. I used the same FSLeyes-based approach for all three files. However, I will point out that all 3 files are now at about the same file size (85K), so maybe the 2 files were compressed beforehand somehow? I don't quite understand...)

Fixes #26.

jcohenadad commented 11 months ago

We will also need to update the labeling convention

joshuacwnewton commented 11 months ago

I've updated the label value to use 60, as per the comment on the issue. I will also be using this value in the tutorial.

joshuacwnewton commented 11 months ago

I'm going to merge this PR and create a pre-release, because not having the available labels is making https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4250 more difficult to review.

This won't be the actual PAM50 release (just a pre-release for review purposes) -- we will create the proper PAM50 release once the outstanding PAM50 spinal level changes have been merged.