Update batch_single_subject.sh for the 2025 SCT Course
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batch_single_subject.sh for the 2025 SCT Course
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Keeping the old syntax will be better for ensuring backwards compatibility with the course data .zips, since we package up the _gmseg and _wmseg files to be used in other tutorials.
CSV generation will fail due to missing labeled seg file.
Superseded by totalspineseg.
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I'll follow up by creating a new dataset release and updating the link in the SCT repo. |
joshuacwnewton
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Jan 12, 2026
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| # Register t2->template with modified parameters (advanced usage of `-param`) | ||
| sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_vert.nii.gz -qc ~/qc_singleSubj -ofolder advanced_param -c t2 -param step=1,type=seg,algo=rigid:step=2,type=seg,metric=CC,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,metric=CC,algo=syn,slicewise=1,iter=2 | ||
| sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_vert.nii.gz -qc ~/qc_singleSubj -ofolder advanced_param -c t2 -param step=1,type=seg,algo=rigid:step=2,type=seg,metric=CC,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,metric=CC,algo=syn,slicewise=1,iter=2 | ||
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| # Register t2->template with large FOV (e.g. C2-L1) using `-ldisc` option | ||
| # sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_seg_labeled_discs.nii.gz -c t2 | ||
| # sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_totalspineseg_discs.nii.gz -c t2 |
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Note to self re: spinalcordtoolbox/spinalcordtoolbox#5023 (comment): Not present in web tutorials? Add?
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Update: No. (This corresponds to the -ldisc page that we removed from the course material due to duplication with the regular -ldisc, and so this should be removed, I think. Large FOVs are already covered by the "how many labels should I use" page?)
joshuacwnewton
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Jan 12, 2026
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| # Compute aSCOR (Adapted Spinal Cord Occupation Ratio) | ||
| # i.e. Spinal cord to canal ratio using the canal seg | ||
| sct_compute_ascor -i-SC t2_seg.nii.gz -i-canal t2_canal_seg.nii.gz -perlevel 1 -o ascor.csv |
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Note to self re: spinalcordtoolbox/spinalcordtoolbox#5023 (comment): Not present in web tutorials? Add?
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Context
In preparation for the upcoming SCT Course, we need to test all of the commands in the SCT Course slide deck.
My approach to testing the commands is to:
batch_single_subject.shcontains exactly the same commands as the SCT Course slide deck.PR description
To make "step 1" easier, this PR adds:
sct_commands (from both the slides and the scripts) and compares them.