From 79e29dfc34896829c8b952a926cde825305de721 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Thu, 31 May 2007 15:07:16 +0000
Subject: [PATCH] *** empty log message ***
---
siena | 2 ++
sienax | 3 ++-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/siena b/siena
index 9669ae2..a2f30bb 100755
--- a/siena
+++ b/siena
@@ -101,6 +101,8 @@ sdo="${sdo}${is_t2}"
echo "---------- extract brain --------------------------------------------" >> ${A}_to_${B}.siena
${FSLDIR}/bin/bet $A ${A}_brain -s -m $betopts >> ${A}_to_${B}.siena
${FSLDIR}/bin/bet $B ${B}_brain -s -m $betopts >> ${A}_to_${B}.siena
+${FSLDIR}/bin/avwmaths++ ${A}_brain -sub `$FSLDIR/bin/avwstats++ ${A}_brain -p 0` -mas ${A}_brain_mask ${A}_brain -odt float
+${FSLDIR}/bin/avwmaths++ ${B}_brain -sub `$FSLDIR/bin/avwstats++ ${B}_brain -p 0` -mas ${B}_brain_mask ${B}_brain -odt float
echo "" >> ${A}_to_${B}.siena
echo "---------- register brains and skulls -------------------------------" >> ${A}_to_${B}.siena
diff --git a/sienax b/sienax
index ec9b43f..107ad81 100755
--- a/sienax
+++ b/sienax
@@ -101,7 +101,8 @@ if [ $regional = 1 ] ; then
fi
echo "---------- extract brain --------------------------------------------" >> ${I}.sienax
-${FSLDIR}/bin/bet $I ${I}_brain -s $betopts >> ${I}.sienax
+${FSLDIR}/bin/bet $I ${I}_brain -s -m $betopts >> ${I}.sienax
+${FSLDIR}/bin/avwmaths++ ${I}_brain -sub `$FSLDIR/bin/avwstats++ ${I}_brain -p 0` -mas ${I}_brain_mask ${I}_brain -odt float
echo "" >> ${I}.sienax
echo "---------- register to stdairach space using brain and skull --------" >> ${I}.sienax
--
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