From e7679ee3c621afdcc8ed479c1297aace01a3beb3 Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Wed, 26 Jun 2013 09:39:05 +0000
Subject: [PATCH] Change name of mean_fsamples to mean_fsumsamples and add FSL
PATH to some commands
---
bedpostx_postproc.sh | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/bedpostx_postproc.sh b/bedpostx_postproc.sh
index c4afa02..55b3fdb 100755
--- a/bedpostx_postproc.sh
+++ b/bedpostx_postproc.sh
@@ -30,11 +30,11 @@ do
done
if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/mean_f1samples` -eq 1 ];then
- ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsamples
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsumsamples
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_fsumsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsumsamples
fib=$(($fib + 1))
done
fi
@@ -63,13 +63,13 @@ 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_slices
rm -f ${subjdir}/data_slice_*
rm -f ${subjdir}/nodif_brain_mask_slice_*
- if [ `imtest ${subjdir}/grad_dev_slice_0000` -eq 1 ];then
+ if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev_slice_0000` -eq 1 ];then
rm -f ${subjdir}/grad_dev_slice_*
fi
fi
--
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