diff --git a/scripts/process_data.sh b/scripts/process_data.sh index 4e57828..23b0562 100755 --- a/scripts/process_data.sh +++ b/scripts/process_data.sh @@ -49,7 +49,7 @@ cd ${SUBJECT_SESSION}/anat/ SUBJECT="${SUBJECT}_${SESSION}" # T1 image file name -T1_image=$(find . -type f -name "*_MPRAGE.nii.gz" -print | head -n 1) +T1_image=$(find . -type f -name "*_UNIT1.nii.gz" -print | head -n 1) # Contrast agnostic segmentation sct_deepseg -i "$T1_image" -task seg_sc_contrast_agnostic -o "${T1_image%.nii.gz}_seg.nii.gz" -qc ${PATH_QC} -qc-subject ${SUBJECT}