Update script and tutorial datasets for PR #5197#36
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This should save us from having to ever manually update CSVs again.
- mismatches between single-subject and multi-subject CSVs - missing truncation on mtr_in_wm.csv
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Tested! Merging so that I can create the actual release. |
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…CT Course (#5197) ## Description This PR updates the web tutorials to match the changes that were made in: - spinalcordtoolbox/sct_tutorial_data#33 Specifically, the diff for [`batch_single_subject.sh`](https://github.com/spinalcordtoolbox/sct_tutorial_data/pull/33/changes#diff-bf79b667b525e00b983d8538154723e006d36c500444390dc24f8b64c379e494) is used to guide the following changes: - `sct_label_vertebrae` -> `sct_deepseg spine` * `-vertfile` -> `-discfile` * `-l` -> `-ldisc` - `sct_deepseg_gm` -> `sct_deepseg graymatter` - Add missing lumbar QC command - Add missing aSCOR command All together, I think these changes are largely straightforward and should be easy to match 1:1 to the script/course changes from last year. This PR also makes some small fixes here and there when noticed: - Improved instructions for `sct_analyze_lesion -f label` (removed confusing `-f label_T2w`) ## Remaining TODOs - [ ] Update all CSV values displayed in the web tutorials with the most up-to-date CSV metrics from the CI. - [ ] The `sct_compute_compresion` tutorial still uses `sct_label_vertebrae` (in the course as well) -- maybe a follow-up change for the 2026 Course? - [ ] The `batch_single_subject.sh` changes include a new cropping prior to `sc_epi`, but this model isn't used in the tutorials. Should we add a tutorial for it? ## Concurrent changes - spinalcordtoolbox/doc-figures@d28af2e - spinalcordtoolbox/sct_tutorial_data#36 ## Built documentation - https://spinalcordtoolbox--5197.org.readthedocs.build/5197/ ## Linked issues Fixes #5012. Fixes #5139.
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I'm going to point the release workflow at this PR and generate the asset zips to test the changes on the SCT side of things, then we can merge..