From 0d82233d2cfc7daa8fdb2f11a48bde676aed8b04 Mon Sep 17 00:00:00 2001
From: Mathieu Guay-Paquet <mathieu.guay-paquet@polymtl.ca>
Date: Wed, 21 Feb 2024 16:56:00 -0500
Subject: [PATCH] Revert "add code to fix csf orientation and pixdim to
 correspond with image native space"

This reverts commit 79e7157a149fe8a73af5d9f18ec3ccfad9ccc901.
---
 code/fix-orientation-derivatives.sh | 92 -----------------------------
 1 file changed, 92 deletions(-)
 delete mode 100644 code/fix-orientation-derivatives.sh

diff --git a/code/fix-orientation-derivatives.sh b/code/fix-orientation-derivatives.sh
deleted file mode 100644
index 2dbf857aa4..0000000000
--- a/code/fix-orientation-derivatives.sh
+++ /dev/null
@@ -1,92 +0,0 @@
-#!/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 "~~~"