From 978cf3d18b9694ecec76a25db0f4afb083e1dffd Mon Sep 17 00:00:00 2001
From: Tim Behrens <behrens@fmrib.ox.ac.uk>
Date: Wed, 29 Sep 2004 17:33:20 +0000
Subject: [PATCH] *** empty log message ***
---
bedpost_datacheck | 26 +++++++++++++-------------
1 file changed, 13 insertions(+), 13 deletions(-)
diff --git a/bedpost_datacheck b/bedpost_datacheck
index f467554..dbefdb4 100755
--- a/bedpost_datacheck
+++ b/bedpost_datacheck
@@ -7,9 +7,9 @@ fi
DIR=$1;
for img in ${DIR}/data ${DIR}/nodif ${DIR}/nodif_brain_mask ;do
- if [ `imtest $img` -eq 1 ] ; then
+ if [ `${FSLDIR}/bin/imtest $img` -eq 1 ] ; then
echo $img
- avwinfo $img;
+ ${FSLDIR}/bin/avwinfo $img;
echo ""
else
echo $img does not exist;
@@ -18,30 +18,30 @@ done
for bv in ${DIR}/bvals ${DIR}/bvecs;do
echo " num lines in $bv "
- cat $bv|wc -l |grep -v "^ *$"
+ cat $bv |grep -v "^ *$"|wc -l
echo " num words in $bv "
cat $bv|wc -w
done
-if [ `imtest ${DIR}/data` -eq 1 -a `imtest ${DIR}/nodif_brain_mask` -eq 1 ];then
+if [ `${FSLDIR}/bin/imtest ${DIR}/data` -eq 1 -a `${FSLDIR}/bin/imtest ${DIR}/nodif_brain_mask` -eq 1 ];then
- dx=`avwval ${DIR}/data dim1`
- dy=`avwval ${DIR}/data dim2`
- dz=`avwval ${DIR}/data dim3`
- dt=`avwval ${DIR}/data dim4`
+ dx=`${FSLDIR}/bin/avwval ${DIR}/data dim1`
+ dy=`${FSLDIR}/bin/avwval ${DIR}/data dim2`
+ dz=`${FSLDIR}/bin/avwval ${DIR}/data dim3`
+ dt=`${FSLDIR}/bin/avwval ${DIR}/data dim4`
- nbmx=`avwval ${DIR}/nodif_brain_mask dim1`
- nbmy=`avwval ${DIR}/nodif_brain_mask dim2`
- nbmz=`avwval ${DIR}/nodif_brain_mask dim3`
+ nbmx=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim1`
+ nbmy=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim2`
+ nbmz=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim3`
if [ $dx -ne $nbmx -o $dy -ne $nbmy -o $dz -ne $nbmz ];then
echo "data dimensions do not match mask dimensions"
fi
- bvallen=`cat ${DIR}/bvals|wc -w|grep -v "^ *$"`
+ bvallen=`cat ${DIR}/bvals|grep -v "^ *$"|wc -w`
bveclenw=`cat ${DIR}/bvecs|wc -w`
- bveclenl=`cat ${DIR}/bvecs|wc -l|grep -v "^ *$"`
+ bveclenl=`cat ${DIR}/bvecs|grep -v "^ *$"|wc -l`
bveclen=`echo "$bveclenw / $bveclenl"|bc`
--
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