Lots of gzip script compatibility updates

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

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*

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*
+

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
 

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