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Merge pull request #5 from sct-pipeline/mb/KI
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Modified name files following BIDS #2
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Mathilde-16 authored Jul 26, 2024
2 parents e06ff0b + 18c0a94 commit af7d83c
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion scripts/process_data.sh
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ cd ${SUBJECT_SESSION}/anat/
SUBJECT="${SUBJECT}_${SESSION}"

# T1 image file name
T1_image=$(find . -type f -name "*_UNIT1.nii.gz" -print | head -n 1)
T1_image=$(find . -type f -name "*_acq-mprage_T1w.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}
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