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Tumour seg

Merged Tumour seg
tumour_seg into main
Merged Saad Jbabdi requested to merge tumour_seg into main
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spinal_dmri_pipeline/scripts/spinal_preproc.sh
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@@ -175,7 +175,7 @@ $sctbin/sct_deepseg_sc -i `$FSLDIR/bin/imglob -extension $D/T2w/t2.nii.gz` -c t2
$sctbin/sct_deepseg_sc -i `$FSLDIR/bin/imglob -extension $D/T2w/t2.nii.gz` -c t2 -o $D/T2w/t2_seg_no_tumour.nii.gz -kernel 3d -qc $D/T2w -thr -1
# Label vertebrae
$sctbin/sct_label_vertebrae -i $D/T2w/t2.nii.gz -s $D/T2w/t2_seg.nii.gz -c t2 -ofolder $D/T2w
$sctbin/sct_label_vertebrae -i $D/T2w/t2.nii.gz -s $D/T2w/t2_seg_no_tumour.nii.gz -c t2 -ofolder $D/T2w
# When there is a tumour, try to detect it and add it to the mask