diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh index 7b167b2..e933d9a 100755 --- a/single_subject/batch_single_subject.sh +++ b/single_subject/batch_single_subject.sh @@ -367,7 +367,7 @@ sct_warp_template -d fmri_moco_mean.nii.gz -w warp_template2fmri.nii.gz -a 0 -qc cd ../t1 # Segment T1-weighted image (to be used in later steps) -sct_deepseg -task seg_sc_contrast_agnostic -i t1.nii.gz +sct_deepseg -task seg_sc_contrast_agnostic -i t1.nii.gz -qc ~/qc_singleSubj/ # Smooth spinal cord along centerline (extracted from the segmentation) sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz