diff --git a/siena b/siena
index 8db468baec60783332aa5262bcd153d5a923d8c5..be58a991bd1456657db0b1b493f0a29892fba701 100755
--- a/siena
+++ b/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 +23,17 @@ Usage() {
exit
}
+if [ _$FSLDIR = _ ] ; then
+ FSLDIR=/usr/local/fsl
+ export FSLDIR
+fi
+
[ "$1" = "" ] && Usage
[ "$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 +45,6 @@ echo "" >
shift 2
-if [ _$FSLDIR = _ ] ; then
- FSLDIR=/usr/local/fsl
- export FSLDIR
-fi
debug=0
betf=0.5
@@ -182,22 +183,22 @@ ${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 \
+ /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}_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.???
fi
diff --git a/siena_cal b/siena_cal
index 540b5d3797490baf3c7e6d55bf99e561a63571e7..5e2f2af87f72e975b8c931e26cc487770cb64809 100755
--- a/siena_cal
+++ b/siena_cal
@@ -4,7 +4,7 @@
#
# Stephen Smith, FMRIB Image Analysis Group
#
-# Copyright (C) 1999-2001 University of Oxford
+# Copyright (C) 1999-2004 University of Oxford
#
# SHCOPYRIGHT
@@ -13,17 +13,18 @@ Usage() {
exit 1
}
-[ "$1" = "" ] && Usage
-[ "$2" = "" ] && Usage
-[ ! -f $1.hdr ] && Usage
-
if [ _$FSLDIR = _ ] ; then
FSLDIR=/usr/local/fsl
export FSLDIR
fi
-input=$1
-inputB=$2
+[ "$1" = "" ] && Usage
+[ "$2" = "" ] && Usage
+[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
+input=`${FSLDIR}/bin/remove_ext $1`
+
+inputB=`${FSLDIR}/bin/remove_ext $2`
+
m=$3
M=`echo "5 k 1.0 $m / p" | dc -`
shift 3
@@ -54,12 +55,13 @@ 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
-/bin/cp -f ${input}.hdr sc${input}.hdr
-/bin/cp -f ${input}.img sc${input}.img
-/bin/cp -f ${input}_brain_mask.hdr sc${input}_brain_mask.hdr
-/bin/cp -f ${input}_brain_mask.img sc${input}_brain_mask.img
-/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
+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/siena_diff ${input} sc${input} $@ > ${input}_to_sc${input}.siena
@@ -70,16 +72,16 @@ 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 \
+/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}_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
+ ${input}_valid_mask_with_sc${input}.hdr* ${input}_valid_mask_with_sc${input}.img* \
+ ${input}_halfwayto_sc${input}_valid_mask.hdr* ${input}_halfwayto_sc${input}_valid_mask.img*
diff --git a/siena_flirt b/siena_flirt
index 6719eea39b66e3e4811ef28533d3e1f849d143b5..105c3da661918779aeb051f2fe17d6ea4a43b53d 100755
--- a/siena_flirt
+++ b/siena_flirt
@@ -4,47 +4,52 @@
#
# Stephen Smith, FMRIB Image Analysis Group
#
-# Copyright (C) 1999-2001 University of Oxford
+# Copyright (C) 1999-2004 University of Oxford
#
# SHCOPYRIGHT
+
Usage() {
echo "Usage: siena_flirt <input1_fileroot> <input2_fileroot>"
exit 1
}
-[ "$1" = "" ] && Usage
-[ "$2" = "" ] && Usage
-[ ! -f $1.hdr ] && Usage
-[ ! -f $2.hdr ] && Usage
-
if [ _$FSLDIR = _ ] ; then
FSLDIR=/usr/local/fsl
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 $2`;
+
+
# register using brains and skulls
-${FSLDIR}/bin/pairreg $1_brain $2_brain $1_brain_skull $2_brain_skull $2_to_$1.mat
-${FSLDIR}/bin/pairreg $2_brain $1_brain $2_brain_skull $1_brain_skull $1_to_$2.mat
+${FSLDIR}/bin/pairreg ${A1}_brain ${A2}_brain ${A1}_brain_skull ${A2}_brain_skull ${A2}_to_${A1}.mat
+${FSLDIR}/bin/pairreg ${A2}_brain ${A1}_brain ${A2}_brain_skull ${A1}_brain_skull ${A1}_to_${A2}.mat
# replace both transforms with "average" (reduces error level AND makes system symmetric)
-F=$1_to_$2.mat
-B=$2_to_$1.mat
+F=${A1}_to_${A2}.mat
+B=${A2}_to_${A1}.mat
${FSLDIR}/bin/convert_xfm -matonly -concat $B -omat tmp_${F}_then_${B} $F
-${FSLDIR}/bin/avscale tmp_${F}_then_${B} $1 > tmp_${F}_then_${B}.avscale
+${FSLDIR}/bin/avscale tmp_${F}_then_${B} ${A1} > tmp_${F}_then_${B}.avscale
${FSLDIR}/bin/extracttxt Backward tmp_${F}_then_${B}.avscale 4 1 > tmp_${F}_then_${B}_halfback
${FSLDIR}/bin/convert_xfm -matonly -concat tmp_${F}_then_${B}_halfback -omat $F $F
${FSLDIR}/bin/convert_xfm -inverse -matonly -omat $B $F
/bin/rm tmp_${F}_then_${B} tmp_${F}_then_${B}.avscale tmp_${F}_then_${B}_halfback
# replace the .mat matrix that takes 2->1 with one that takes 2->halfway and one that takes 1->halfway
-${FSLDIR}/bin/avscale $2_to_$1.mat $1_brain > $2_to_$1.mat_avscale
-${FSLDIR}/bin/extracttxt Forward $2_to_$1.mat_avscale 4 1 > $2_halfwayto_$1.mat
-${FSLDIR}/bin/extracttxt Backward $2_to_$1.mat_avscale 4 1 > $1_halfwayto_$2.mat
+${FSLDIR}/bin/avscale ${A2}_to_${A1}.mat ${A1}_brain > ${A2}_to_${A1}.mat_avscale
+${FSLDIR}/bin/extracttxt Forward ${A2}_to_${A1}.mat_avscale 4 1 > ${A2}_halfwayto_${A1}.mat
+${FSLDIR}/bin/extracttxt Backward ${A2}_to_${A1}.mat_avscale 4 1 > ${A1}_halfwayto_${A2}.mat
# produce picture for registration evaluation
-${FSLDIR}/bin/flirt -out $1_halfwayto_$2 -applyxfm -init $1_halfwayto_$2.mat -ref $1 -in $1_brain
-${FSLDIR}/bin/flirt -out $2_halfwayto_$1 -applyxfm -init $2_halfwayto_$1.mat -ref $1 -in $2_brain
-${FSLDIR}/bin/slicer $2_halfwayto_$1 $1_halfwayto_$2 -s 1 -x 0.4 gr$1$2a -x 0.5 gr$1$2b -x 0.6 gr$1$2c -y 0.4 gr$1$2d -y 0.5 gr$1$2e -y 0.6 gr$1$2f -z 0.4 gr$1$2g -z 0.5 gr$1$2h -z 0.6 gr$1$2i
-${FSLDIR}/bin/convert -colors 100 +append gr$1$2a gr$1$2b gr$1$2c gr$1$2d gr$1$2e gr$1$2f gr$1$2g gr$1$2h gr$1$2i $2_regto_$1.gif
-/bin/rm gr$1$2a gr$1$2b gr$1$2c gr$1$2d gr$1$2e gr$1$2f gr$1$2g gr$1$2h gr$1$2i $2_halfwayto_$1.img $2_halfwayto_$1.hdr $1_halfwayto_$2.img $1_halfwayto_$2.hdr
+${FSLDIR}/bin/flirt -out ${A1}_halfwayto_${A2} -applyxfm -init ${A1}_halfwayto_${A2}.mat -ref ${A1} -in ${A1}_brain
+${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*
+
diff --git a/siena_flow2tal b/siena_flow2tal
index 81a8d4ead84edfd0b28f81fb1857597362054368..9651b2c0e9d02304f1466ddd61e64fb2fe820bfd 100755
--- a/siena_flow2tal
+++ b/siena_flow2tal
@@ -4,29 +4,30 @@
#
# Stephen Smith, FMRIB Image Analysis Group
#
-# Copyright (C) 2002-2003 University of Oxford
+# Copyright (C) 2002-2004 University of Oxford
#
# SHCOPYRIGHT
+
Usage() {
echo "Usage: sienal <fileroot2> <fileroot2> [-d]"
echo "-d : debug (don't delete intermediate files)"
exit
}
-[ "$1" = "" ] && Usage
-[ "$2" = "" ] && Usage
-[ ! -f $1.hdr ] && Usage
-[ ! -f $2.hdr ] && Usage
-A=$1
-B=$2
-shift 2
-
if [ _$FSLDIR = _ ] ; then
FSLDIR=/usr/local/fsl
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`;
+shift 2
+
debug=0
for opts in $@ ; do
@@ -39,7 +40,7 @@ done
# register to MNI152 if not already done, and create halfway2tal transform
if [ ! -f ${A}_to_tal.mat ] ; then
- if [ ! -f ${A}_brain.hdr ] ; then
+ if [ `${FSLDIR}/bin/imtest ${A}_brain` = 0 ] ; then
${FSLDIR}/bin/bet $A ${A}_brain
fi
${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_to_tal.mat
@@ -56,6 +57,6 @@ ${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 ${A}_brain.hdr* ${A}_brain.img ${A}_to_${B}_flow_dil.hdr* ${A}_to_${B}_flow_dil.img
fi
diff --git a/sienax b/sienax
index 70440ebb33962ee6484c0a8ef5ae648b83a955e0..8e646a2170de1639bbf5ebdf0e6c1fdbea41f4a1 100755
--- a/sienax
+++ b/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
@@ -201,7 +201,7 @@ 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 \
+ /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
fi