Added processing script

scripts/process_data.sh

@@ -0,0 +1,78 @@
+#!/bin/sh
+
+
+# The following global variables are retrieved from the caller sct_run_batch
+# but could be overwritten by uncommenting the lines below:
+#PATH_DATA_PROCESSED="~/data_processed"
+#PATH_RESULTS="~/results"
+#PATH_LOG="~/log"
+#PATH_QC="~/qc"
+
+
+# Uncomment for full verbose
+set -x
+
+# Immediately exit if error
+# set -e -o pipefail
+
+# Retrieve input params
+SUBJECT_SESSION=$1
+
+# get starting time:
+start=`date +%s`
+
+
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Update SUBJECT variable to the prefix for BIDS file names, considering the "ses" entity
+SUBJECT=`cut -d "/" -f1 <<< "$SUBJECT_SESSION"`
+SESSION=`cut -d "/" -f2 <<< "$SUBJECT_SESSION"`
+
+
+# Go to folder where data will be copied and processed
+cd $PATH_DATA_PROCESSED
+
+# Copy list of participants in processed data folder
+if [[ ! -f "participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv .
+fi
+
+# Copy source images
+mkdir -p $SUBJECT
+rsync -avzh --copy-links $PATH_DATA/$SUBJECT_SESSION $SUBJECT/
+
+# Go to anat folder where all structural data are located
+cd ${SUBJECT_SESSION}/anat/
+
+# Update SUBJECT variable to the prefix for BIDS file names, considering the "ses" entity
+SUBJECT="${SUBJECT}_${SESSION}"
+
+# T1 image file name
+T1_image=$(find . -type f -name "*_MPRAGE.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 ${SUBJECT}
+
+# Detect ponto-medullary junction
+sct_detect_pmj -i "$T1_image" -c t1 -s "${T1_image%.nii.gz}_seg.nii.gz" -qc ${PATH_QC} -qc-subject ${SUBJECT}
+
+# Compute average cord CSA at 64mm distance from the PMJ (which roughtly corresponds to C2-C3 disc, according to https://www.frontiersin.org/journals/neuroimaging/articles/10.3389/fnimg.2022.1031253/full)
+# normalize them to PAM50 ('-normalize-PAM50' flag)
+sct_process_segmentation -i "${T1_image%.nii.gz}_seg.nii.gz" -pmj "${T1_image%.nii.gz}_pmj.nii.gz" -pmj-distance 64 -perslice 0 -o ${PATH_RESULTS}/csa-SC_T1w.csv -append 1 -qc ${PATH_QC} -qc-subject ${SUBJECT} -qc-image "$T1_image"
+
+# Go back to parent folder
+cd ..
+
+
+# Display useful info for the log
+end=`date +%s`
+runtime=$((end-start))
+echo
+echo "~~~"
+echo "SCT version: `sct_version`"
+echo "Ran on:      `uname -nsr`"
+echo "Duration:    $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
+echo "~~~"
+
+