diff --git a/multi_subject/process_data.sh b/multi_subject/process_data.sh index 457e6bf..0d5b645 100755 --- a/multi_subject/process_data.sh +++ b/multi_subject/process_data.sh @@ -80,7 +80,7 @@ segment_if_does_not_exist() { if [[ -e "${FILESEGMANUAL}" ]]; then echo "Found! Using manual segmentation." rsync -avzh "${FILESEGMANUAL}" "${FILESEG}".nii.gz - sct_qc -i "${file}".nii.gz -s "${FILESEG}".nii.gz -p sct_deepseg -qc "${PATH_QC}" -qc-subject "${SUBJECT}" + sct_qc -i "${file}".nii.gz -s "${FILESEG}".nii.gz -p sct_deepseg_sc -qc "${PATH_QC}" -qc-subject "${SUBJECT}" else echo "Not found. Proceeding with automatic segmentation." # Segment spinal cord