From 672bff263aa27937b139e894d1a789f14ed972c5 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Thu, 26 Aug 2004 16:08:39 +0000
Subject: [PATCH] *** empty log message ***
---
doc/siena | 57 +++++++++++++++++++++++++-------------------------
doc/sienax | 20 +++++++++---------
siena | 38 ++++++++++++++++-----------------
siena_cal | 41 +++++++++++++++++-------------------
siena_diff.c | 19 +----------------
siena_flirt | 8 +++----
siena_flow2tal | 7 +++----
sienax | 4 ++--
8 files changed, 86 insertions(+), 108 deletions(-)
diff --git a/doc/siena b/doc/siena
index 8db468b..ec68a13 100755
--- a/doc/siena
+++ b/doc/siena
@@ -4,7 +4,7 @@
#
# Stephen Smith, FMRIB Image Analysis Group
#
-# Copyright (C) 1999-2002 University of Oxford
+# Copyright (C) 1999-2004 University of Oxford
#
# SHCOPYRIGHT
@@ -23,12 +23,16 @@ Usage() {
exit
}
-[ "$1" = "" ] && Usage
+if [ _$FSLDIR = _ ] ; then
+ FSLDIR=/usr/local/fsl
+ export FSLDIR
+fi
+
[ "$2" = "" ] && Usage
-[ ! -f $1.hdr ] && Usage
-[ ! -f $2.hdr ] && Usage
-A=$1
-B=$2
+[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
+[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
+A=`${FSLDIR}/bin/remove_ext $1`
+B=`${FSLDIR}/bin/remove_ext $2`
echo "-----------------------------------------------------------------------" > ${A}_to_${B}.siena
echo "" >> ${A}_to_${B}.siena
@@ -40,10 +44,6 @@ echo "" >
shift 2
-if [ _$FSLDIR = _ ] ; then
- FSLDIR=/usr/local/fsl
- export FSLDIR
-fi
debug=0
betf=0.5
@@ -182,24 +182,25 @@ ${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow -mul -1 ${A}_to_${B}_flowneg
${FSLDIR}/bin/overlay 0 0 ${A}_halfwayto_${B} -a ${A}_to_${B}_flow 0.01 1 ${A}_to_${B}_flowneg 0.01 1 ${A}_halfwayto_${B}_render
if [ $debug = 0 ] ; then
- /bin/rm -f ${A}_brain.hdr ${A}_brain.img ${A}_brain_mask.hdr ${A}_brain_mask.img ${A}_brain_skull.hdr ${A}_brain_skull.img \
- ${B}_brain.hdr ${B}_brain.img ${B}_brain_mask.hdr ${B}_brain_mask.img ${B}_brain_skull.hdr ${B}_brain_skull.img \
- ${A}_halfwayto_${B}.hdr ${A}_halfwayto_${B}.img ${A}_halfwayto_${B}_mask.hdr ${A}_halfwayto_${B}_mask.img \
- ${B}_halfwayto_${A}.hdr ${B}_halfwayto_${A}.img ${B}_halfwayto_${A}_mask.hdr ${B}_halfwayto_${A}_mask.img \
- ${A}_halfwayto_${B}_talmask.hdr ${A}_halfwayto_${B}_talmask.img \
- ${B}_halfwayto_${A}_talmask.hdr ${B}_halfwayto_${A}_talmask.img \
- ${A}_halfwayto_${B}_brain.hdr ${A}_halfwayto_${B}_brain.img \
- ${A}_halfwayto_${B}_brain_seg.hdr ${A}_halfwayto_${B}_brain_seg.img \
- ${A}_to_${B}_flowneg.hdr ${A}_to_${B}_flowneg.img \
- ${B}_halfwayto_${A}_brain.hdr ${B}_halfwayto_${A}_brain.img \
- ${B}_halfwayto_${A}_brain_seg.hdr ${B}_halfwayto_${A}_brain_seg.img \
- ${B}_to_${A}_flowneg.hdr ${B}_to_${A}_flowneg.img \
- ${B}_to_${A}.mat_avscale \
- ${A}_halfwayto_${B}_brain.vol ${B}_halfwayto_${A}_brain.vol \
- ${A}_talmask.hdr ${A}_talmask.img ${B}_talmask.hdr ${B}_talmask.img \
- ${A}_and_${B}_talmask.hdr ${A}_and_${B}_talmask.img \
- ${A}_to_tal_inv.mat ${B}_to_tal_inv.mat ${A}_to_${B}_tmp.mat \
- ${A}_valid_mask.??? ${B}_valid_mask.??? ${A}_valid_mask_to_${B}.??? ${B}_valid_mask_to_${A}.??? ${A}_valid_mask_with_$B.??? ${B}_valid_mask_with_$A.??? ${A}_halfwayto_${B}_valid_mask.??? ${B}_halfwayto_${A}_valid_mask.???
+ $FSLDIR/bin/imrm ${A}_brain.* ${A}_brain_mask.* ${A}_brain_skull.* \
+ ${B}_brain.* ${B}_brain_mask.* ${B}_brain_skull.* \
+ ${A}_halfwayto_${B}.* ${A}_halfwayto_${B}_mask.* \
+ ${B}_halfwayto_${A}.* ${B}_halfwayto_${A}_mask.* \
+ ${A}_halfwayto_${B}_talmask.* \
+ ${B}_halfwayto_${A}_talmask.* \
+ ${A}_halfwayto_${B}_brain.* \
+ ${A}_halfwayto_${B}_brain_seg.* \
+ ${A}_to_${B}_flowneg.* \
+ ${B}_halfwayto_${A}_brain.* \
+ ${B}_halfwayto_${A}_brain_seg.* \
+ ${B}_to_${A}_flowneg.* \
+ ${A}_talmask.* ${B}_talmask.* \
+ ${A}_and_${B}_talmask.* \
+ ${A}_valid_mask.* ${B}_valid_mask.* ${A}_valid_mask_to_${B}.* ${B}_valid_mask_to_${A}.* ${A}_valid_mask_with_$B.* ${B}_valid_mask_with_$A.* ${A}_halfwayto_${B}_valid_mask.* ${B}_halfwayto_${A}_valid_mask.*
+ /bin/rm -f ${A}_to_tal_inv.mat ${B}_to_tal_inv.mat ${A}_to_${B}_tmp.mat \
+ ${A}_halfwayto_${B}_brain.vol ${B}_halfwayto_${A}_brain.vol \
+ ${B}_to_${A}.mat_avscale
fi
echo "$pbvc_average"
+
diff --git a/doc/sienax b/doc/sienax
index 70440eb..cec4b3d 100755
--- a/doc/sienax
+++ b/doc/sienax
@@ -4,7 +4,7 @@
#
# Stephen Smith, FMRIB Image Analysis Group
#
-# Copyright (C) 1999-2002 University of Oxford
+# Copyright (C) 1999-2004 University of Oxford
#
# SHCOPYRIGHT
@@ -24,9 +24,14 @@ Usage() {
exit
}
+if [ _$FSLDIR = _ ] ; then
+ FSLDIR=/usr/local/fsl
+ export FSLDIR
+fi
+
[ _$1 = _ ] && Usage
-[ ! -f $1.hdr ] && Usage
-I=$1
+I=`${FSLDIR}/bin/remove_ext $1`;
+[ `${FSLDIR}/bin/imtest $I` = 0 ] && Usage
echo "-----------------------------------------------------------------------" > ${I}.sienax
echo "" >> ${I}.sienax
@@ -38,11 +43,6 @@ echo "" >
shift
-if [ _$FSLDIR = _ ] ; then
- FSLDIR=/usr/local/fsl
- export FSLDIR
-fi
-
debug=0
regional=0
betf=0.5
@@ -201,8 +201,8 @@ if [ $regional = 1 ] ; then
fi
if [ $debug = 0 ] ; then
- /bin/rm -f ${I}_brain.hdr ${I}_brain.img ${I}_brain_skull.hdr ${I}_brain_skull.img \
- ${I}_talmask* ${I}2tal.avscale ${I}2tal_inv.mat
+ /bin/rm -f `$FSLDIR/bin/imglob ${I}_brain* ${I}_talmask*`
+ /bin/rm -f ${I}2tal.avscale ${I}2tal_inv.mat
fi
echo "$brain"
diff --git a/siena b/siena
index be58a99..ec68a13 100755
--- a/siena
+++ b/siena
@@ -28,7 +28,6 @@ if [ _$FSLDIR = _ ] ; then
export FSLDIR
fi
-[ "$1" = "" ] && Usage
[ "$2" = "" ] && Usage
[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
@@ -183,24 +182,25 @@ ${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow -mul -1 ${A}_to_${B}_flowneg
${FSLDIR}/bin/overlay 0 0 ${A}_halfwayto_${B} -a ${A}_to_${B}_flow 0.01 1 ${A}_to_${B}_flowneg 0.01 1 ${A}_halfwayto_${B}_render
if [ $debug = 0 ] ; then
- /bin/rm -f ${A}_brain.hdr* ${A}_brain.img* ${A}_brain_mask.hdr* ${A}_brain_mask.img* ${A}_brain_skull.hdr* ${A}_brain_skull.img* \
- ${B}_brain.hdr* ${B}_brain.img* ${B}_brain_mask.hdr* ${B}_brain_mask.img* ${B}_brain_skull.hdr* ${B}_brain_skull.img* \
- ${A}_halfwayto_${B}.hdr* ${A}_halfwayto_${B}.img* ${A}_halfwayto_${B}_mask.hdr* ${A}_halfwayto_${B}_mask.img* \
- ${B}_halfwayto_${A}.hdr* ${B}_halfwayto_${A}.img* ${B}_halfwayto_${A}_mask.hdr* ${B}_halfwayto_${A}_mask.img* \
- ${A}_halfwayto_${B}_talmask.hdr* ${A}_halfwayto_${B}_talmask.img* \
- ${B}_halfwayto_${A}_talmask.hdr* ${B}_halfwayto_${A}_talmask.img* \
- ${A}_halfwayto_${B}_brain.hdr* ${A}_halfwayto_${B}_brain.img* \
- ${A}_halfwayto_${B}_brain_seg.hdr* ${A}_halfwayto_${B}_brain_seg.img* \
- ${A}_to_${B}_flowneg.hdr* ${A}_to_${B}_flowneg.img* \
- ${B}_halfwayto_${A}_brain.hdr* ${B}_halfwayto_${A}_brain.img* \
- ${B}_halfwayto_${A}_brain_seg.hdr* ${B}_halfwayto_${A}_brain_seg.img* \
- ${B}_to_${A}_flowneg.hdr* ${B}_to_${A}_flowneg.img* \
- ${B}_to_${A}.mat_avscale \
- ${A}_halfwayto_${B}_brain.vol ${B}_halfwayto_${A}_brain.vol \
- ${A}_talmask.hdr* ${A}_talmask.img* ${B}_talmask.hdr* ${B}_talmask.img* \
- ${A}_and_${B}_talmask.hdr* ${A}_and_${B}_talmask.img* \
- ${A}_to_tal_inv.mat ${B}_to_tal_inv.mat ${A}_to_${B}_tmp.mat \
- ${A}_valid_mask.??? ${B}_valid_mask.??? ${A}_valid_mask_to_${B}.??? ${B}_valid_mask_to_${A}.??? ${A}_valid_mask_with_$B.??? ${B}_valid_mask_with_$A.??? ${A}_halfwayto_${B}_valid_mask.??? ${B}_halfwayto_${A}_valid_mask.???
+ $FSLDIR/bin/imrm ${A}_brain.* ${A}_brain_mask.* ${A}_brain_skull.* \
+ ${B}_brain.* ${B}_brain_mask.* ${B}_brain_skull.* \
+ ${A}_halfwayto_${B}.* ${A}_halfwayto_${B}_mask.* \
+ ${B}_halfwayto_${A}.* ${B}_halfwayto_${A}_mask.* \
+ ${A}_halfwayto_${B}_talmask.* \
+ ${B}_halfwayto_${A}_talmask.* \
+ ${A}_halfwayto_${B}_brain.* \
+ ${A}_halfwayto_${B}_brain_seg.* \
+ ${A}_to_${B}_flowneg.* \
+ ${B}_halfwayto_${A}_brain.* \
+ ${B}_halfwayto_${A}_brain_seg.* \
+ ${B}_to_${A}_flowneg.* \
+ ${A}_talmask.* ${B}_talmask.* \
+ ${A}_and_${B}_talmask.* \
+ ${A}_valid_mask.* ${B}_valid_mask.* ${A}_valid_mask_to_${B}.* ${B}_valid_mask_to_${A}.* ${A}_valid_mask_with_$B.* ${B}_valid_mask_with_$A.* ${A}_halfwayto_${B}_valid_mask.* ${B}_halfwayto_${A}_valid_mask.*
+ /bin/rm -f ${A}_to_tal_inv.mat ${B}_to_tal_inv.mat ${A}_to_${B}_tmp.mat \
+ ${A}_halfwayto_${B}_brain.vol ${B}_halfwayto_${A}_brain.vol \
+ ${B}_to_${A}.mat_avscale
fi
echo "$pbvc_average"
+
diff --git a/siena_cal b/siena_cal
index 5e2f2af..71eb4d2 100755
--- a/siena_cal
+++ b/siena_cal
@@ -18,11 +18,9 @@ if [ _$FSLDIR = _ ] ; then
export FSLDIR
fi
-[ "$1" = "" ] && Usage
[ "$2" = "" ] && Usage
[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
input=`${FSLDIR}/bin/remove_ext $1`
-
inputB=`${FSLDIR}/bin/remove_ext $2`
m=$3
@@ -55,13 +53,9 @@ echo "0.0 $M 0.0 $t2" >> sc${input}_halfwayto_${input}.mat
echo "0.0 0.0 $M $t3" >> sc${input}_halfwayto_${input}.mat
echo "0.0 0.0 0.0 1.0" >> sc${input}_halfwayto_${input}.mat
-ftmp=`echo ${input}.hdr*`; /bin/cp -f $ftmp sc${ftmp}
-ftmp=`echo ${input}.img*`; /bin/cp -f $ftmp sc${ftmp}
-ftmp=`echo ${input}_brain_mask.hdr*`; /bin/cp -f $ftmp sc${ftmp}
-ftmp=`echo ${input}_brain_mask.img*`; /bin/cp -f $ftmp sc${ftmp}
-# the following works but is dodge (copying .hdr.gz to .hdr potentially)
-/bin/cp -f ${input}_valid_mask_with_${inputB}.hdr* ${input}_valid_mask_with_sc${input}.hdr
-/bin/cp -f ${input}_valid_mask_with_${inputB}.img* ${input}_valid_mask_with_sc${input}.img
+$FSLDIR/bin/imcp $input sc$input
+$FSLDIR/bin/imcp ${input}_brain_mask sc${input}_brain_mask
+$FSLDIR/bin/imcp ${input}_valid_mask_with_$inputB ${input}_valid_mask_with_sc$input
${FSLDIR}/bin/siena_diff ${input} sc${input} $@ > ${input}_to_sc${input}.siena
@@ -72,16 +66,19 @@ corr=`echo "10 k $vm $cal / p" | dc -`
#echo "$m $vm $cal $corr"
echo $corr
-/bin/rm -f sc${input}.hdr* sc${input}.img* sc${input}_brain_mask.hdr* sc${input}_brain_mask.img* \
- ${input}_halfwayto_sc${input}.hdr* ${input}_halfwayto_sc${input}.img* \
- ${input}_halfwayto_sc${input}_brain.hdr* ${input}_halfwayto_sc${input}_brain.img* \
- ${input}_halfwayto_sc${input}_brain_seg.hdr* ${input}_halfwayto_sc${input}_brain_seg.img* \
- ${input}_halfwayto_sc${input}_mask.hdr* ${input}_halfwayto_sc${input}_mask.img* \
- ${input}_halfwayto_sc${input}_talmask.hdr* ${input}_halfwayto_sc${input}_talmask.img* \
- sc${input}_halfwayto_${input}.hdr* sc${input}_halfwayto_${input}.img* \
- sc${input}_halfwayto_${input}_mask.hdr* sc${input}_halfwayto_${input}_mask.img* \
- ${input}_halfwayto_sc${input}.mat sc${input}_halfwayto_${input}.mat \
- ${input}_to_sc${input}_flow.hdr* ${input}_to_sc${input}_flow.img* \
- ${input}_to_sc${input}.siena ${input}_halfwayto_sc${input}_brain.vol \
- ${input}_valid_mask_with_sc${input}.hdr* ${input}_valid_mask_with_sc${input}.img* \
- ${input}_halfwayto_sc${input}_valid_mask.hdr* ${input}_halfwayto_sc${input}_valid_mask.img*
+$FSLDIR/bin/imrm sc${input}.* \
+ sc${input}_brain_mask.* \
+ ${input}_halfwayto_sc${input}.* \
+ ${input}_halfwayto_sc${input}_brain.* \
+ ${input}_halfwayto_sc${input}_brain_seg.* \
+ ${input}_halfwayto_sc${input}_mask.* \
+ ${input}_halfwayto_sc${input}_talmask.* \
+ sc${input}_halfwayto_${input}.* \
+ sc${input}_halfwayto_${input}_mask.* \
+ ${input}_to_sc${input}_flow.* \
+ ${input}_valid_mask_with_sc${input}.* \
+ ${input}_halfwayto_sc${input}_valid_mask.*
+
+/bin/rm -f ${input}_halfwayto_sc${input}.mat sc${input}_halfwayto_${input}.mat \
+ ${input}_to_sc${input}.siena ${input}_halfwayto_sc${input}_brain.vol
+
diff --git a/siena_diff.c b/siena_diff.c
index fe916ec..db3b36e 100644
--- a/siena_diff.c
+++ b/siena_diff.c
@@ -566,8 +566,7 @@ arr2 = arr2 + 5*(CORRWIDTH+SEARCH);
{
FILE *tmpfp;
- sprintf(thestring,"%s_halfwayto_%s_brain_seg.hdr",argv[1],argv[2]);
-
+ /* sprintf(thestring,"%s_halfwayto_%s_brain_seg.hdr",argv[1],argv[2]);*/
/* if((tmpfp=fopen(thestring,"rb"))==NULL)*/ /* test for existing segmentation output */
if(1)
{
@@ -864,22 +863,6 @@ if (flow_output)
printf("RATIO %.4f mm\n", (total*voxel_volume) / (count*voxel_area) ); /* mean perpendicular edge motion; l in the equations */
printf("PBVC %.4f %%\n", (calib*30*total*voxel_volume) / (count*voxel_area) );
-/* }}} */
-
- /* {{{ COMMENT remove resampled intermediate files */
-
-#ifdef FoldingComment
-
-if ( ! debug )
-{
- sprintf(thestring,"/bin/rm -f %s_halfwayto_%s.img %s_halfwayto_%s.hdr %s_halfwayto_%s.img %s_halfwayto_%s.hdr %s_halfwayto_%s_mask.* %s_halfwayto_%s_mask.* %s_halfwayto_%s_brain.img %s_halfwayto_%s_brain.hdr %s_halfwayto_%s_brain_seg.img %s_halfwayto_%s_brain_seg.hdr",
- argv[1],argv[2],argv[1],argv[2],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2],argv[2],argv[1],
- argv[1],argv[2],argv[1],argv[2],argv[1],argv[2],argv[1],argv[2]);
- system(thestring);
-}
-
-#endif
-
/* }}} */
return 0;
diff --git a/siena_flirt b/siena_flirt
index 105c3da..929f61b 100755
--- a/siena_flirt
+++ b/siena_flirt
@@ -19,13 +19,11 @@ if [ _$FSLDIR = _ ] ; then
export FSLDIR
fi
-[ "$1" = "" ] && Usage
[ "$2" = "" ] && Usage
[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
-A1=`${FSLDIR}/bin/remove_ext $1`;
-A2=`${FSLDIR}/bin/remove_ext $2`;
-
+A1=`${FSLDIR}/bin/remove_ext $1`
+A2=`${FSLDIR}/bin/remove_ext $2`
# register using brains and skulls
${FSLDIR}/bin/pairreg ${A1}_brain ${A2}_brain ${A1}_brain_skull ${A2}_brain_skull ${A2}_to_${A1}.mat
@@ -51,5 +49,5 @@ ${FSLDIR}/bin/flirt -out ${A1}_halfwayto_${A2} -applyxfm -init ${A1}_halfwayto_$
${FSLDIR}/bin/flirt -out ${A2}_halfwayto_${A1} -applyxfm -init ${A2}_halfwayto_${A1}.mat -ref ${A1} -in ${A2}_brain
${FSLDIR}/bin/slicer ${A2}_halfwayto_${A1} ${A1}_halfwayto_${A2} -s 1 -x 0.4 gr${A1}${A2}a -x 0.5 gr${A1}${A2}b -x 0.6 gr${A1}${A2}c -y 0.4 gr${A1}${A2}d -y 0.5 gr${A1}${A2}e -y 0.6 gr${A1}${A2}f -z 0.4 gr${A1}${A2}g -z 0.5 gr${A1}${A2}h -z 0.6 gr${A1}${A2}i
${FSLDIR}/bin/convert -colors 100 +append gr${A1}${A2}a gr${A1}${A2}b gr${A1}${A2}c gr${A1}${A2}d gr${A1}${A2}e gr${A1}${A2}f gr${A1}${A2}g gr${A1}${A2}h gr${A1}${A2}i ${A2}_regto_${A1}.gif
-/bin/rm gr${A1}${A2}a gr${A1}${A2}b gr${A1}${A2}c gr${A1}${A2}d gr${A1}${A2}e gr${A1}${A2}f gr${A1}${A2}g gr${A1}${A2}h gr${A1}${A2}i ${A2}_halfwayto_${A1}.img* ${A2}_halfwayto_${A1}.hdr* ${A1}_halfwayto_${A2}.img* ${A1}_halfwayto_${A2}.hdr*
+/bin/rm gr${A1}${A2}a gr${A1}${A2}b gr${A1}${A2}c gr${A1}${A2}d gr${A1}${A2}e gr${A1}${A2}f gr${A1}${A2}g gr${A1}${A2}h gr${A1}${A2}i `$FSLDIR/bin/imglob ${A2}_halfwayto_${A1}.* ${A1}_halfwayto_${A2}.*`
diff --git a/siena_flow2tal b/siena_flow2tal
index 9651b2c..e8cb8ee 100755
--- a/siena_flow2tal
+++ b/siena_flow2tal
@@ -20,12 +20,11 @@ if [ _$FSLDIR = _ ] ; then
export FSLDIR
fi
-[ "$1" = "" ] && Usage
[ "$2" = "" ] && Usage
[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
-A=`${FSLDIR}/bin/remove_ext $1`;
-B=`${FSLDIR}/bin/remove_ext $2`;
+A=`${FSLDIR}/bin/remove_ext $1`
+B=`${FSLDIR}/bin/remove_ext $2`
shift 2
debug=0
@@ -57,6 +56,6 @@ ${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_tal -mas ${FSLDIR}/etc/standard/avg1
# cleanup
if [ $debug = 0 ] ; then
- /bin/rm -f ${A}_halfwayto_${B}_inv.mat ${A}_brain.hdr* ${A}_brain.img ${A}_to_${B}_flow_dil.hdr* ${A}_to_${B}_flow_dil.img
+ /bin/rm -f ${A}_halfwayto_${B}_inv.mat `$FSLDIR/bin/imglob ${A}_brain.* ${A}_to_${B}_flow_dil.*`
fi
diff --git a/sienax b/sienax
index 8e646a2..cec4b3d 100755
--- a/sienax
+++ b/sienax
@@ -201,8 +201,8 @@ if [ $regional = 1 ] ; then
fi
if [ $debug = 0 ] ; then
- /bin/rm -f ${I}_brain.hdr* ${I}_brain.img* ${I}_brain_skull.hdr* ${I}_brain_skull.img* \
- ${I}_talmask* ${I}2tal.avscale ${I}2tal_inv.mat
+ /bin/rm -f `$FSLDIR/bin/imglob ${I}_brain* ${I}_talmask*`
+ /bin/rm -f ${I}2tal.avscale ${I}2tal_inv.mat
fi
echo "$brain"
--
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