Add MS lesion segmentation data (#32)

Author: plbenveniste

single_subject/batch_single_subject.sh

@@ -398,7 +398,7 @@ sct_flatten_sagittal -i t1.nii.gz -s t1_seg.nii.gz
 # New features (SCT v6.5, December 2024)
 # ======================================================================================================================
 
-# Lesion analysis for SCI and MS lesions
+# Lesion analysis for SCI
 cd ../t2_lesion
 # Segment the spinal cord and intramedullary lesion using the SCIsegV2 model
 # Note: t2.nii.gz contains a fake lesion for the purpose of this tutorial
@@ -409,11 +409,6 @@ sct_deepseg lesion_sci_t2 -i t2.nii.gz -qc ~/qc_singleSubj
 # Check results using FSLeyes
 fsleyes t2.nii.gz -cm greyscale t2_sc_seg.nii.gz -cm red -a 70.0 t2_lesion_seg.nii.gz -cm blue-lightblue -a 70.0 &
 
-# Note: We also have a contrast-agnostic segmentation command for MS lesions, too:
-sct_deepseg lesion_ms -i t2.nii.gz -qc ~/qc_singleSubj
-# As well as a segmentation command tailored to MP2RAGE MS lesions
-# sct_deepseg lesion_ms_mp2rage -i t2.nii.gz -qc ~/qc_singleSubj
-
 # Compute various morphometric measures, such as number of lesions, lesion length, lesion volume, etc.
 sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -qc ~/qc_singleSubj
 # Lesion analysis using PAM50 (the -f flag is used to specify the folder containing the atlas/template)
@@ -442,5 +437,14 @@ sct_deepseg rootlets -i t2.nii.gz -qc ~/qc_singleSubj
 # Check results using FSLeyes
 fsleyes t2.nii.gz -cm greyscale t2_rootlets.nii.gz -cm subcortical -a 70.0 &
 
+# Multiple sclerosis lesion segmentation on T2-weighted images
+cd ../t2_ms/
+# Segment the spinal cord (to be used as input for lesion_ms QC)
+sct_deepseg spinalcord -i t2.nii.gz -qc ~/qc_singleSubj
+# Segment using lesion_ms (-single-fold is recommended to speed up inference time)
+sct_deepseg lesion_ms -i t2.nii.gz -qc ~/qc_singleSubj -qc-seg t2_seg.nii.gz -single-fold
+# Check results using FSLeyes
+fsleyes t2.nii.gz -cm greyscale t2_lesion_seg.nii.gz -cm red -a 70.0 &
+
 # Return to parent directory
 cd ..

single_subject/data/t2_ms/t2.nii.gz

@@ -8,6 +8,7 @@ data_normalizing-morphometrics-compression,single_subject/data/t2_compression/t2
 data_normalizing-morphometrics-compression,single_subject/data/t2_compression/t2_compressed_seg_labeled.nii.gz
 data_normalizing-morphometrics-compression,single_subject/data/t2_compression/t2_compressed_labels-compression.nii.gz
 data_lesion-analysis,single_subject/data/t2_lesion/t2.nii.gz
+data_ms-lesion-segmentation,single_subject,single_subject/data/t2_ms/t2.nii.gz
 data_template-registration,single_subject/data/t2/t2.nii.gz
 data_template-registration,single_subject/data/t2/t2_seg.nii.gz
 data_template-registration,single_subject/data/t2/t2_labels_vert.nii.gz