From 6d277c12fef2f1d0361239993bbf208f00c7e34d Mon Sep 17 00:00:00 2001
From: Julian McGinnis <julian.mcginnis@tum.de>
Date: Wed, 10 Aug 2022 15:06:33 +0200
Subject: [PATCH 1/2] add wrapper script for fsl-based data orientation

---
 source/utility/reorient.sh | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100755 source/utility/reorient.sh

diff --git a/source/utility/reorient.sh b/source/utility/reorient.sh
new file mode 100755
index 0000000..09bed5b
--- /dev/null
+++ b/source/utility/reorient.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+#
+# Reorient sagittally scanned MRI images to axial orientation, complying to
+#
+# the stitching convention of the stitching algorithm by Ben Glocker.
+#
+# Usage:
+#   ./reorient.sh <SCAN>
+#
+# Authors: Julian McGinnis
+
+# Retrieve input params
+SCAN=$1
+
+# assemble name
+SCAN_NAME=${SCAN%%.*}
+FILE_ENDING="_axial_ornt.nii.gz"
+FILE_PATH="$SCAN_NAME$FILE_ENDING"
+
+echo "Creating $FILE_PATH"
+
+# get starting time:
+start=`date +%s`
+
+echo "Swaping Dimensions"
+fslswapdim ${SCAN} LR AP IS ${FILE_PATH}
+echo "Forcing neuological orientation"
+fslorient -forceneurological ${FILE_PATH}
+
+# Display useful info for the log
+end=`date +%s`
+runtime=$((end-start))
+echo "Duration: $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"

From 754aace058f8b597a427fb961dad0008c959e9a4 Mon Sep 17 00:00:00 2001
From: Julian McGinnis <33037028+jqmcginnis@users.noreply.github.com>
Date: Thu, 11 Aug 2022 08:15:48 +0200
Subject: [PATCH 2/2] Update source/utility/reorient.sh
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

fix typo

Co-authored-by: Sandrine Bédard <71230552+sandrinebedard@users.noreply.github.com>
---
 source/utility/reorient.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/source/utility/reorient.sh b/source/utility/reorient.sh
index 09bed5b..bab5203 100755
--- a/source/utility/reorient.sh
+++ b/source/utility/reorient.sh
@@ -24,7 +24,7 @@ start=`date +%s`
 
 echo "Swaping Dimensions"
 fslswapdim ${SCAN} LR AP IS ${FILE_PATH}
-echo "Forcing neuological orientation"
+echo "Forcing neurological orientation"
 fslorient -forceneurological ${FILE_PATH}
 
 # Display useful info for the log