Add script to get centerline from SC segmentation

scripts/get_centerline_from_segmentation.sh

@@ -0,0 +1,119 @@
+#!/bin/bash
+#
+# Get centerline from manually corrected T2w segmentation ground truth (GT) for CanProCo dataset
+#
+# Dependencies (versions):
+# - SCT (5.8)
+#
+
+# Usage:
+#     sct_run_batch -c config.json
+
+# 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"
+#
+# Author: Jan Valosek
+#
+
+# Uncomment for full verbose
+set -x
+
+# Immediately exit if error
+set -e -o pipefail
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Print retrieved variables from sct_run_batch to the log (to allow easier debug)
+echo "Retrieved variables from from the caller sct_run_batch:"
+echo "PATH_DATA: ${PATH_DATA}"
+echo "PATH_DATA_PROCESSED: ${PATH_DATA_PROCESSED}"
+echo "PATH_RESULTS: ${PATH_RESULTS}"
+echo "PATH_LOG: ${PATH_LOG}"
+echo "PATH_QC: ${PATH_QC}"
+
+# Retrieve input params and other params
+SUBJECT=$1
+
+# get starting time:
+start=`date +%s`
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Go to folder where data will be copied and processed
+cd $PATH_DATA_PROCESSED
+
+# Copy BIDS-required files to processed data folder (e.g. list of participants)
+if [[ ! -f "participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv .
+fi
+# Copy list of participants in results folder 
+if [[ ! -f "participants.json" ]]; then
+  rsync -avzh $PATH_DATA/participants.json .
+fi
+if [[ ! -f "dataset_description.json" ]]; then
+  rsync -avzh $PATH_DATA/dataset_description.json .
+fi
+
+# Copy source images
+# Note: we use '/./' in order to include the sub-folder 'ses-0X'
+rsync -Ravzh $PATH_DATA/./$SUBJECT .
+# Go to subject folder for source images
+cd ${SUBJECT}/anat
+
+# Define variables
+# We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+file="${SUBJECT//[\/]/_}"
+
+# -------------------------------------------------------------------------
+# T2w
+# -------------------------------------------------------------------------
+# Add suffix corresponding to contrast
+file_t2w=${file}_T2w
+# Construct path to manually corrected SC segmentation
+FILESEG="${file_t2w}_seg"
+FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${FILESEG}-manual.nii.gz"
+
+# Check if T2w SC seg exists
+if [[ -f ${FILESEGMANUAL} ]];then
+
+    # Copy manually corrected segmentation ground truth (GT) from derivatives folder (to do not alter files in derivatives)
+    # Note, this ground truth (GT) segmentation was obtained from reoriented and resampled images (this is why we are applying the same preprocessing steps also below)
+    rsync -avzh ${FILESEGMANUAL} ${FILESEG}.nii.gz
+    # Fit a regularized centerline on an already-existing cord segmentation.
+    sct_get_centerline -i ${FILESEG}.nii.gz -method fitseg -qc ${PATH_QC} -qc-subject ${SUBJECT}
+    # Copy centerline to derivatives folder (to be compatible with ivadomed)
+    mkdir -p ${PATH_DATA_PROCESSED}/derivatives/labels/${SUBJECT}/anat
+    rsync -avzh ${FILESEG}_centerline.nii.gz ${PATH_DATA_PROCESSED}/derivatives/labels/${SUBJECT}/anat/${FILESEG}_centerline.nii.gz
+
+    # Apply the same preprocessing steps as were done for the SC segmentation (to have the same dimensions of the image and GT centerline)
+    # Rename raw file
+    mv ${file_t2w}.nii.gz ${file_t2w}_raw.nii.gz
+    # Reorient to RPI and resample to 0.8mm isotropic voxel (supposed to be the effective resolution)
+    sct_image -i ${file_t2w}_raw.nii.gz -setorient RPI -o ${file_t2w}_raw_RPI.nii.gz
+    sct_resample -i ${file_t2w}_raw_RPI.nii.gz -mm 0.8x0.8x0.8 -o ${file_t2w}_raw_RPI_r.nii.gz
+    # Rename _raw_RPI_r file (to be BIDS compliant)
+    mv ${file_t2w}_raw_RPI_r.nii.gz ${file_t2w}.nii.gz
+
+else
+    echo "${SUBJECT}/${FILESEGMANUAL} does not exist" >> $PATH_LOG/_error_check_input_files.log
+fi
+
+# -------------------------------------------------------------------------
+# Display useful info for the log
+# -------------------------------------------------------------------------
+end=`date +%s`
+runtime=$((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 "~~~"