batch_single_subject.sh: Comment out -f command (needs reg)

Author: joshuacwnewton

single_subject/batch_single_subject.sh

@@ -422,8 +422,10 @@ sct_deepseg -i t2.nii.gz -task seg_sc_lesion_t2w_sci -qc ~/qc_singleSubj
 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 &
 # 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)
-sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -f label_T2w -qc ~/qc_singleSubj
+# Note: You must go through the "Register to Template" steps (labeling, registration) first
+# sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -f label -qc ~/qc_singleSubj
 
 # Note: We also have a contrast-agnostic segmentation command for MS lesions, too:
 sct_deepseg -i t2.nii.gz -task seg_ms_lesion -qc ~/qc_singleSubj