From 46b15b2b6ff3ee644bcf0cc2ba2103b6e0ee1704 Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Fri, 17 May 2013 10:11:54 +0000
Subject: [PATCH] Add path FSLDIR/bin when use imtest and fslmaths
---
CUDA/bedpostx_postproc_gpu.sh | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/CUDA/bedpostx_postproc_gpu.sh b/CUDA/bedpostx_postproc_gpu.sh
index acccbfc..ba93e37 100644
--- a/CUDA/bedpostx_postproc_gpu.sh
+++ b/CUDA/bedpostx_postproc_gpu.sh
@@ -36,7 +36,7 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/mean_f1samples` -eq 1 ];then
fib=1
while [ $fib -le $numfib ]
do
- fslmaths ${subjdir}.bedpostX/mean_fsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsamples
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_fsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsamples
fib=$(($fib + 1))
done
fi
@@ -45,11 +45,11 @@ fi
echo Removing intermediate files
-if [ `imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
- if [ `imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
- if [ `imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
+if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
+ if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
+ if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
rm -rf ${subjdir}.bedpostX/diff_parts
- if [ `imtest ${subjdir}.bedpostX/grad_dev_slice_0000` -eq 1 ];then
+ if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/grad_dev_slice_0000` -eq 1 ];then
rm -f ${subjdir}.bedpostX/grad_dev_slice_*
fi
fi
--
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