Explore/add new compression metrics #19
Description
Originally posted as part of spinalcordtoolbox/spinalcordtoolbox#3733 (comment) -- moving here because the original SCT/#3733 issue eventually focused mainly on normalization to PAM50 and was closed by successfully merging SCT/#4003.
The project aims to add new relevant metrics to assess cervical spinal cord compression for degenerative cervical myelopathy.
Possible ref for triangular compression: 10.1093/brain/118.1.263
Other possible metrics
CSA for R-L
Compute CSA for right and left spinal cord by seperating from mid-point of R-L diameter.
TODO: Check in scikit-image how to extract the mid point (we use scikit-image to get the axes for AP/RL diam, so it’s a matter of fetching more outputs from that library)
Triangular compression
Compression can also have a triangular shape. However, metrics like symmetry/solidity would not be able to detect this compression.
Proposition:
- With the spinal cord segmentation, scale compressed spinal cord to PAM50 using CSA.
- Register to PAM50 template (center of mass or centermassrot)
- Compute similarity metric (Dice, Hausdorff )
TODO: Make sure there isn’t a metric that can already assess this triangulation (another that is currently not implemented in process_seg)
