From 0a3eb4b1c6c6f9275b32eeb9dd06f631d7524697 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Tue, 19 Oct 2004 15:08:32 +0000
Subject: [PATCH] *** empty log message ***
---
sienax | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/sienax b/sienax
index e95e5e5..1a7a022 100755
--- a/sienax
+++ b/sienax
@@ -150,10 +150,15 @@ if [ $nseg = 2 ] ; then
xb=`echo $S | awk '{print $3}'`
brain=`echo "2 k $xa $xb * $vscale * p" | dc -`
else
+ if [ _$lm != _ ] ; then
+ ${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_talmaskbrain ${I}_talmaskbrain
+ fi
+
${FSLDIR}/bin/fast $imtype -e -ov $@ ${I}_talmaskbrain >> ${I}.sienax 2>&1
if [ _$lm != _ ] ; then
- ${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_talmaskbrain_pve_1 ${I}_talmaskbrain_pve_1
+ ${FSLDIR}/bin/avwmaths_32R $lm -bin -max ${I}_talmaskbrain_pve_2 ${I}_talmaskbrain_pve_2
+ ${FSLDIR}/bin/avwmaths_32SI $lm -bin -mul 3 -max ${I}_talmaskbrain_seg ${I}_talmaskbrain_seg
fi
echo "" >> ${I}.sienax
--
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