add code to fix csf orientation and pixdim to correspond with image n…

…ative space

code/fix-orientation-derivatives.sh

@@ -0,0 +1,92 @@
+#!/bin/bash
+#
+# Fixes orientation of derivatives labels
+#
+# Usage:
+#   ./process_data.sh <SUBJECT>
+#
+#
+# Authors: Sandrine Bédard
+# 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
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Retrieve input 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 source images
+rsync -avzh $PATH_DATA/$SUBJECT .
+
+# Go to anat folder where all structural data are located
+cd ${SUBJECT}/anat/
+
+file_t2="${SUBJECT}_T2w"
+
+
+orient_native=`sct_image -i ${file_t2}.nii.gz -getorient | cut -f18 -d' '`
+orient_native=${orient_native:9:5}
+echo "Native orientation: $orient_native"
+
+
+
+# Copy CSF seg
+file_t2_csf="${file_t2}_label-CSF_seg"
+rsync -avzh $PATH_DATA/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz ${file_t2_csf}_or.nii.gz
+# Set to CSF seg to native orientation
+sct_image -i ${file_t2_csf}_or.nii.gz -setorient $orient_native -o ${file_t2_csf}_reorient.nii.gz
+
+
+# Resample no native resolution:
+
+sct_resample -i ${file_t2_csf}_reorient.nii.gz -ref ${file_t2}.nii.gz -x linear -o ${file_t2_csf}_reorient_r.nii.gz
+sct_maths -i ${file_t2_csf}_reorient_r.nii.gz -bin 0.5 -o ${file_t2_csf}_reorient_r_bin.nii.gz
+
+# Create QC report
+sct_qc -i ${file_t2}.nii.gz -s ${file_t2_csf}_reorient_r_bin.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
+
+# Create derivatives:
+mkdir -p $PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/
+rsync -avzh ${file_t2_csf}_reorient_r_bin.nii.gz $PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz
+
+
+# Verify presence of output files and write log file if error
+# ------------------------------------------------------------------------------
+FILES_TO_CHECK=(
+  "$PATH_DATA_PROCESSED/derivatives/labels/${SUBJECT}/anat/${file_t2_csf}.nii.gz"
+)
+pwd
+for file in ${FILES_TO_CHECK[@]}; do
+  if [[ ! -e $file ]]; then
+    echo "${SUBJECT}/anat/${file} does not exist" >> $PATH_LOG/_error_check_output_files.log
+  fi
+done
+
+# Display useful info for the log
+end=`date +%s`
+runtime=$((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 "~~~"