From 741619656a31f2516b0fe0378602f2468d0a2a1c Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Fri, 10 Feb 2006 05:47:39 +0000
Subject: [PATCH] CVS:
----------------------------------------------------------------------
---
sienax | 23 +++++++----------------
1 file changed, 7 insertions(+), 16 deletions(-)
diff --git a/sienax b/sienax
index c913f09..7eff770 100755
--- a/sienax
+++ b/sienax
@@ -156,6 +156,8 @@ else
echo "" >> ${I}.sienax
echo "---------- convert brain volume into normalised volume --------------" >> ${I}.sienax
+ echo "" >> ${I}.sienax
+ echo "tissue volume unnormalised-volume" >> ${I}.sienax
if [ $regional = 1 ] ; then
${FSLDIR}/bin/avwmaths_32R ${I}_talmaskbrain_pve_1 -mas ${I}_talmask_segperiph ${I}_talmaskbrain_pve_1_segperiph
S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_1_segperiph -m -v`
@@ -163,9 +165,7 @@ else
xb=`echo $S | awk '{print $3}'`
uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
- echo "" >> ${I}.sienax
- echo "unnormalised-pgrey $uxg" >> ${I}.sienax
- echo "pgrey $xg" >> ${I}.sienax
+ echo "pgrey $xg $uxg (peripheral grey)" >> ${I}.sienax
${FSLDIR}/bin/avwmaths_32R ${I}_talmaskbrain_pve_0 -mas ${I}_talmask_segvent ${I}_talmaskbrain_pve_0_segvent
S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_0_segvent -m -v`
@@ -173,34 +173,25 @@ else
xb=`echo $S | awk '{print $3}'`
uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
- echo "" >> ${I}.sienax
- echo "unnormalised-vcsf $uxg" >> ${I}.sienax
- echo "vcsf $xg" >> ${I}.sienax
+ echo "vcsf $xg $uxg (ventricular CSF)" >> ${I}.sienax
fi
S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_1 -m -v`
xa=`echo $S | awk '{print $1}'`
xb=`echo $S | awk '{print $3}'`
ugrey=`echo "2 k $xa $xb * 1 / p" | dc -`
ngrey=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
- echo "" >> ${I}.sienax
- echo "unnormalised-GREY $ugrey" >> ${I}.sienax
- echo "GREY $ngrey" >> ${I}.sienax
+ echo "GREY $ngrey $ugrey" >> ${I}.sienax
S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_2 -m -v`
xa=`echo $S | awk '{print $1}'`
xb=`echo $S | awk '{print $3}'`
uwhite=`echo "2 k $xa $xb * 1 / p" | dc -`
nwhite=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
- echo "" >> ${I}.sienax
- echo "unnormalised-WHITE $uwhite" >> ${I}.sienax
- echo "WHITE $nwhite" >> ${I}.sienax
+ echo "WHITE $nwhite $uwhite" >> ${I}.sienax
fi
ubrain=`echo "2 k $uwhite $ugrey + 1 / p" | dc -`
nbrain=`echo "2 k $nwhite $ngrey + 1 / p" | dc -`
-echo "" >> ${I}.sienax
-echo "unnormalised-BRAIN $ubrain" >> ${I}.sienax
-echo "BRAIN $nbrain" >> ${I}.sienax
-echo "" >> ${I}.sienax
+echo "BRAIN $nbrain $ubrain" >> ${I}.sienax
${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_talmaskbrain_seg 1.9 5 ${I}_render
--
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