spinalcordtoolbox / PAM50

https://github.com/neuropoly/spinalcordtoolbox
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Inconsistent X-Y location of labels for `PAM50_label_body.nii.gz` #22

Open jcohenadad opened 1 year ago

jcohenadad commented 1 year ago

Context

From forum post: https://forum.spinalcordmri.org/t/registration-of-lumbar-data-to-pam50/1109

While working with the labels I saw that the PAM_label_body usually places the label at 70/70/xx but labels 15:18,20 are at 70/71/xx, so one voxel more anterior. Maybe this is intentional but it looked a bit unusual.

The reason for this inconsistency is likely because labels were created at the center of mass of the cord segmentation, which happens to be slightly shifted along the A-P direction depending on the S-I location.

Solution

We could re-generate all labels, making sure they are centered at x=70, y=70.

Pros:

Cons:

Important We should make sure that, if other PAM50 label files are also affected by this problem, we also fix them in the same PR.

jcohenadad commented 11 months ago

Alternatively, remove that file, see https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4229

Also related to https://github.com/spinalcordtoolbox/PAM50/issues/25