batch_single_subject.sh: add QC and Fsleyes command for the lesion an…

…alysis section

single_subject/batch_single_subject.sh

@@ -119,11 +119,14 @@ sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_
 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
-sct_deepseg -i t2.nii.gz -task seg_sc_lesion_t2w_sci
+sct_deepseg -i t2.nii.gz -task seg_sc_lesion_t2w_sci -qc ~/qc_singleSubj
 # Note: Two files are output:
 # - t2_sc_seg.nii.gz: the spinal cord segmentation
 # - t2_lesion_seg.nii.gz: the lesion segmentation
 
+# 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 &
+
 # 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