From 3d45978b8a0a016dd85230b9b01aed737a0bd296 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Wed, 1 Aug 2007 17:24:03 +0000
Subject: [PATCH] remove nodif
---
bedpostx | 7 +------
bedpostx_preproc.sh | 2 +-
2 files changed, 2 insertions(+), 7 deletions(-)
diff --git a/bedpostx b/bedpostx
index ebf7df1..9202f23 100755
--- a/bedpostx
+++ b/bedpostx
@@ -17,7 +17,7 @@ Usage() {
echo "Usage: bedpostx <subject directory> [options]"
echo ""
echo "expects to find bvals and bvecs in subject directory"
- echo "expects to find data nodif_brain_mask nodif in subject directory"
+ echo "expects to find data and nodif_brain_mask in subject directory"
echo "options:"
echo "-n (number of fibres per voxel, default 2)"
echo "-w (ARD weight, more weight means less fibres killed per voxel, default 1)"
@@ -83,11 +83,6 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
exit 1
fi
-if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` -eq 0 ]; then
- echo "${subjdir}/nodif not found"
- exit 1
-fi
-
if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
echo "${subjdir}/nodif_brain_mask not found"
exit 1
diff --git a/bedpostx_preproc.sh b/bedpostx_preproc.sh
index bdae346..90123ca 100755
--- a/bedpostx_preproc.sh
+++ b/bedpostx_preproc.sh
@@ -11,7 +11,7 @@ subjdir=$1
echo Copying files to bedpost directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
-${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
+${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
${FSLDIR}/bin/fslmaths\
${subjdir}/nodif\
-mas ${subjdir}/nodif_brain_mask\
--
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