Switch to using T2 warps in dMRI/fMRI tutorials #27
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joshuacwnewton
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Mar 7, 2025
joshuacwnewton
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Mar 10, 2025
## Description When the contrast-agnostic model was changed from MONAI to nnUNet, the method for determining the output suffix also changed, thus the output switched from `_seg.nii.gz` to `_sc_seg.nii.gz`. I think adding the "sc" part makes sense for multiclass models (SC/lesion, SC/GM, etc.). But, for our single-class SC tools (`sct_deepseg_sc`, `sct_propseg`, etc.) we typically just output `_seg.nii.gz`. So, this PR adds a special case to check for single-output SC models, then choose the "basic" suffix accordingly. This PR is being tested in https://github.com/spinalcordtoolbox/sct_tutorial_data/pull/27/files#r1985521419, because that PR is getting blocked by this issue (SCT course was written for `_seg.nii.gz suffix`). ## Linked issues Fixes #4805. Needed for spinalcordtoolbox/sct_tutorial_data#27, which is in turn needed for #4804. --------- Co-authored-by: Mathieu Guay-Paquet <[email protected]>
…model" This reverts commit 769b89f.
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In PR #25 (commit 4893e6f), we switched to using the T2 initwarps. But, we haven't done that for the tutorials yet.