From 20165ae8841545d55bbf5f9baaec5cb3e4d9a5c0 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Thu, 11 Mar 2010 10:11:01 +0000
Subject: [PATCH] back to copying input. this time it's called bvecs_unrotated
---
rotate_bvecs | 26 +++++++++++++-------------
1 file changed, 13 insertions(+), 13 deletions(-)
diff --git a/rotate_bvecs b/rotate_bvecs
index 84216b2..ce0670a 100755
--- a/rotate_bvecs
+++ b/rotate_bvecs
@@ -3,8 +3,7 @@
if [ "$2" == "" ];then
echo ""
echo "Usage: rotate_bvecs <ecclogfile> <bvecs>"
- echo "used to update bvecs based on eddy correction"
- echo "will create a new bvecs file called <bvecs>_rot"
+ echo "will save bvecs file into <bvecs>_unrotated and create new bvecs file called <bvecs>"
echo ""
exit 1
fi
@@ -12,21 +11,22 @@ fi
ecclog=$1
bvecs=$2
-if [ -f ${bvecs}_rot ];then
+if [ -f ${bvecs}_unrotated ];then
echo ""
- echo "Error: Found that ${bvecs}_rot already exists"
- echo "This probably means that you have run this script before."
- echo "To get this program to run, please remove the file ${bvecs}_rot"
+ echo "Error: Found that ${bvecs}_unrotated already exists"
+ echo "This probably means that you have run this script before. Be aware that this also means ${bvecs} have already been rotated!"
+ echo "If you want to force this program to run, please remove the file ${bvecs}_unrotated"
echo ""
exit 1
fi
-
+/bin/cp ${bvecs} ${bvecs}_unrotated
+#/bin/rm -f ${bvecs}
# this only works if the bvecs are in lines...
-Xs=$(cat ${bvecs} | head -1 | tail -1)
-Ys=$(cat ${bvecs} | head -2 | tail -1)
-Zs=$(cat ${bvecs} | head -3 | tail -1)
+Xs=$(cat ${bvecs}_unrotated | head -1 | tail -1)
+Ys=$(cat ${bvecs}_unrotated | head -2 | tail -1)
+Zs=$(cat ${bvecs}_unrotated | head -3 | tail -1)
rnd=${$}
cat ${ecclog} | while read line; do
@@ -96,7 +96,7 @@ for matfile in /tmp/grot${rnd}_*.mat;do
i=$(echo "$i + 1" | bc) ;
done
-echo "$rXs" > ${bvecs}_rot;
-echo "$rYs" >> ${bvecs}_rot;
-echo "$rZs" >> ${bvecs}_rot;
+echo "$rXs" > ${bvecs};
+echo "$rYs" >> ${bvecs};
+echo "$rZs" >> ${bvecs};
--
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