CVS: ----------------------------------------------------------------------

Makefile

@@ -14,13 +14,15 @@ GT_OBJS = groupttest.o
 
 XFILES = siena_diff surface_norm cylsamp groupttest
 
-SCRIPTS = siena siena_flirt siena_cal sienax siena_flow2tal
+SCRIPTS = siena siena_flirt siena_cal sienax siena_flow2std
 
 all:	${XFILES} docscripts
 
 # DON'T REMOVE THE -O0!!!! siena_diff doesn't work with optimisation
 siena_diff: siena_diff.c
 	$(CC) $(CFLAGS) -O0  -DFDT="float" -o siena_diff siena_diff.c $(LDFLAGS) $(LIBS)
+siena_diffCC: siena_diff.cc
+	${CXX} $(LDFLAGS) -o $@ ${SN_OBJS} ${LIBCC}
 
 surface_norm: ${SN_OBJS}
 	${CXX} ${LDFLAGS} -o $@ ${SN_OBJS} ${LIBCC}

doc/index.html

@@ -463,7 +463,7 @@ significantly with age or disease progression.
 <LI> Run <br><code>siena A B</code><br> on all subjects'
 two-timepoints data (here <code>A</code> and <code>B</code>).
 
-<LI> For each subject run <br><code>siena_flow2tal A B</code><br> -
+<LI> For each subject run <br><code>siena_flow2std A B</code><br> -
 this runs flirt to generate the transform to standard space (if it
 doesn't already exist), takes the edge flow (atrophy) image generated
 by <code>siena</code>, dilates this several times (to "thicken" this edge
@@ -471,15 +471,15 @@ flow image), transforms to standard space, and masks with a standard
 space edge mask. It then smooths this with a Gaussian filter of
 half-width 10mm before remasking; you may want to edit this or even
 remove this step - find the call to <code>ip</code> in
-$FSLDIR/bin/siena_flow2tal and change the <code>10</code> or just remove
+$FSLDIR/bin/siena_flow2std and change the <code>10</code> or just remove
 that line.
 
 <LI> All subjects will now have an edge flow image in standard edge
-space called <code>A_to_B_flow_to_tal</code>. Merge these into a single 4D
+space called <code>A_to_B_flow_to_std</code>. Merge these into a single 4D
 image; for example, if each subject's analysis has so far been carried
 out in a subdirectory called siena_subject_*, where the * could be
 subject ID or name, use a command such as:<br><code>
-avwmerge -t flow_all_subjects `imglob -oneperimage siena_subject_*/A_to_B_flow_to_tal*`</code><br>
+avwmerge -t flow_all_subjects `imglob -oneperimage siena_subject_*/A_to_B_flow_to_std*`</code><br>
 
 Note: it is very important that the order that the subjects appear in
 this command matches the order you intend when you then create the

lesions_0.1

@@ -37,12 +37,12 @@ ${FSLDIR}/bin/bet $1 $1_brain -m
 ${FSLDIR}/bin/fast -e -ov $1_brain
 
 # register t1 to standard space and invert transform
-${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in $1_brain -omat $1_brain_2_tal.mat
-${FSLDIR}/bin/convert_xfm -inverse -omat tal_2_$1_brain.mat $1_brain_2_tal.mat
+${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in $1_brain -omat $1_brain_2_std.mat
+${FSLDIR}/bin/convert_xfm -inverse -omat std_2_$1_brain.mat $1_brain_2_std.mat
 
 # dilate (6mm) standard space structural segmentation, bring into t1 space and re-binarise
 ${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dil -dil -dil strucseg_2_$1_brain
-${FSLDIR}/bin/flirt -in strucseg_2_$1_brain -ref $1_brain -out strucseg_2_$1_brain -applyxfm -init tal_2_$1_brain.mat
+${FSLDIR}/bin/flirt -in strucseg_2_$1_brain -ref $1_brain -out strucseg_2_$1_brain -applyxfm -init std_2_$1_brain.mat
 ${FSLDIR}/bin/avwmaths strucseg_2_$1_brain -bin strucseg_2_$1_brain
 
 # produce t1-derived CSF mask and also dilate in-plane: 5 voxels outside central mask, 1 voxel inside mask

lesions_0.2

@@ -53,12 +53,12 @@ ${FSLDIR}/bin/bet $A ${A}_brain -m
 ${FSLDIR}/bin/fast -e -ov ${A}_brain
 
 # register t1 to standard space and invert transform
-${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_brain_2_tal.mat
-${FSLDIR}/bin/convert_xfm -inverse -omat tal_2_${A}_brain.mat ${A}_brain_2_tal.mat
+${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_brain_2_std.mat
+${FSLDIR}/bin/convert_xfm -inverse -omat std_2_${A}_brain.mat ${A}_brain_2_std.mat
 
 # dilate (6mm) standard space ventricles+deep-grey, bring into t1 space and re-binarise to make "CENTRAL MASK"
 ${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dil -dil -dil strucseg_2_${A}_brain
-${FSLDIR}/bin/flirt -in strucseg_2_${A}_brain -ref ${A}_brain -out strucseg_2_${A}_brain -applyxfm -init tal_2_${A}_brain.mat
+${FSLDIR}/bin/flirt -in strucseg_2_${A}_brain -ref ${A}_brain -out strucseg_2_${A}_brain -applyxfm -init std_2_${A}_brain.mat
 ${FSLDIR}/bin/avwmaths strucseg_2_${A}_brain -bin strucseg_2_${A}_brain
 
 # produce t1-derived CSF mask and also dilate in-plane: 5 voxels outside CENTRAL MASK, 1 voxel inside mask

lesions_0.3

@@ -54,12 +54,12 @@ ${FSLDIR}/bin/bet $A ${A}_brain -m
 ${FSLDIR}/bin/fast -e -ov ${A}_brain
 
 # register t1 to standard space and invert transform
-${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_brain_2_tal.mat
-${FSLDIR}/bin/convert_xfm -inverse -omat tal_2_${A}_brain.mat ${A}_brain_2_tal.mat
+${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_brain_2_std.mat
+${FSLDIR}/bin/convert_xfm -inverse -omat std_2_${A}_brain.mat ${A}_brain_2_std.mat
 
 # dilate (6mm) standard space ventricles+deep-grey, bring into t1 space and re-binarise to make "CENTRAL MASK"
 ${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dil -dil -dil strucseg_2_${A}_brain
-${FSLDIR}/bin/flirt -in strucseg_2_${A}_brain -ref ${A}_brain -out strucseg_2_${A}_brain -applyxfm -init tal_2_${A}_brain.mat
+${FSLDIR}/bin/flirt -in strucseg_2_${A}_brain -ref ${A}_brain -out strucseg_2_${A}_brain -applyxfm -init std_2_${A}_brain.mat
 ${FSLDIR}/bin/avwmaths strucseg_2_${A}_brain -bin strucseg_2_${A}_brain
 
 # produce t1-derived CSF mask and also dilate in-plane: 5 voxels outside CENTRAL MASK, 1 voxel inside mask

siena

@@ -50,9 +50,9 @@ debug=0
 betopts=""
 sdopts=""
 sdo="-m"
-dotal=0
-talmask=0
-talroi=""
+dostd=0
+stdmask=0
+stdroi=""
 origin3=37 # `avwval ${FSLDIR}/etc/standard/avg152T1 origin3`
 pixdim3=2  # `avwval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
 
@@ -75,20 +75,20 @@ while [ _$1 != _ ] ; do
 	is_t2=" -s -t2"
         shift
     elif [ $1 = -m ] ; then
-	talmask=1
-	dotal=1
+	stdmask=1
+	dostd=1
         shift
     elif [ $1 = -t ] ; then
-	dotal=1
-	talt=`echo $2 | sed 's/-/_/g'`
-	talt=`echo "10 k $talt $pixdim3 / $origin3 + p" | dc -`
-	talroi="$talroi -roi 0 1000000 0 1000000 0 $talt 0 1"
+	dostd=1
+	stdt=`echo $2 | sed 's/-/_/g'`
+	stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc -`
+	stdroi="$stdroi -roi 0 1000000 0 1000000 0 $stdt 0 1"
 	shift 2
     elif [ $1 = -b ] ; then
-	dotal=1
-	talb=`echo $2 | sed 's/-/_/g'`
-	talb=`echo "10 k $talb $pixdim3 / $origin3 + p" | dc -`
-	talroi="$talroi -roi 0 1000000 0 1000000 $talb 1000000 0 1"
+	dostd=1
+	stdb=`echo $2 | sed 's/-/_/g'`
+	stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc -`
+	stdroi="$stdroi -roi 0 1000000 0 1000000 $stdb 1000000 0 1"
 	shift 2
     else
 	Usage
@@ -122,15 +122,15 @@ ${FSLDIR}/bin/flirt -in ${A}_valid_mask -ref $B -out ${A}_valid_mask_to_${B} -ap
 ${FSLDIR}/bin/avwmaths ${A}_valid_mask -mul ${B}_valid_mask_to_${A} ${A}_valid_mask_with_$B
 ${FSLDIR}/bin/avwmaths ${B}_valid_mask -mul ${A}_valid_mask_to_${B} ${B}_valid_mask_with_$A
 
-if [ $dotal = 1 ] ; then
+if [ $dostd = 1 ] ; then
     echo ""                                                                        >> ${A}_to_${B}.siena
     echo "----------  standard space masking  ----------------------------------" >> ${A}_to_${B}.siena
-    ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_to_tal.mat >> ${A}_to_${B}.siena
-    ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${B}_brain -omat ${B}_to_tal.mat >> ${A}_to_${B}.siena
-    ${FSLDIR}/bin/convert_xfm -inverse -omat ${A}_to_tal_inv.mat ${A}_to_tal.mat
-    ${FSLDIR}/bin/convert_xfm -inverse -omat ${B}_to_tal_inv.mat ${B}_to_tal.mat
+    ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_to_std.mat >> ${A}_to_${B}.siena
+    ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${B}_brain -omat ${B}_to_std.mat >> ${A}_to_${B}.siena
+    ${FSLDIR}/bin/convert_xfm -inverse -omat ${A}_to_std_inv.mat ${A}_to_std.mat
+    ${FSLDIR}/bin/convert_xfm -inverse -omat ${B}_to_std_inv.mat ${B}_to_std.mat
 
-    ${FSLDIR}/bin/convert_xfm -concat ${B}_to_tal_inv.mat -omat ${A}_to_${B}_tmp.mat ${A}_to_tal.mat
+    ${FSLDIR}/bin/convert_xfm -concat ${B}_to_std_inv.mat -omat ${A}_to_${B}_tmp.mat ${A}_to_std.mat
     RMSDIFF=`${FSLDIR}/bin/rmsdiff ${A}_to_${B}.mat ${A}_to_${B}_tmp.mat $A | sed 's/\..*$/ /g'` # last part makes it integer
     echo "rmsdiff for standard space transform is $RMSDIFF mm" >> ${A}_to_${B}.siena
     if [ $RMSDIFF -ge 10 ] ; then
@@ -138,19 +138,19 @@ if [ $dotal = 1 ] ; then
 	echo "Warning! Probably failed consistency check for standard-space registrations!" >> ${A}_to_${B}.siena
     fi
 
-    if [ $talmask = 1 ] ; then
-	${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_brain_mask_dil2 -ref $A -out ${A}_talmask -applyxfm -init ${A}_to_tal_inv.mat
-	${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_brain_mask_dil2 -ref $B -out ${B}_talmask -applyxfm -init ${B}_to_tal_inv.mat
-	${FSLDIR}/bin/avwmaths ${A}_brain_mask -mas ${A}_talmask ${A}_brain_mask
-	${FSLDIR}/bin/avwmaths ${B}_brain_mask -mas ${B}_talmask ${B}_brain_mask
+    if [ $stdmask = 1 ] ; then
+	${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_brain_mask_dil2 -ref $A -out ${A}_stdmask -applyxfm -init ${A}_to_std_inv.mat
+	${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_brain_mask_dil2 -ref $B -out ${B}_stdmask -applyxfm -init ${B}_to_std_inv.mat
+	${FSLDIR}/bin/avwmaths ${A}_brain_mask -mas ${A}_stdmask ${A}_brain_mask
+	${FSLDIR}/bin/avwmaths ${B}_brain_mask -mas ${B}_stdmask ${B}_brain_mask
     fi
 
-    if [ "$talroi" != "" ] ; then
-	${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_brain_mask -mul 0 -add 1 $talroi ${A}_and_${B}_talmask
-	${FSLDIR}/bin/flirt -in ${A}_and_${B}_talmask -ref $A -out ${A}_talmask -applyxfm -init ${A}_to_tal_inv.mat
-	${FSLDIR}/bin/flirt -in ${A}_and_${B}_talmask -ref $B -out ${B}_talmask -applyxfm -init ${B}_to_tal_inv.mat
-	${FSLDIR}/bin/avwmaths ${A}_valid_mask_with_$B -mul ${A}_talmask ${A}_valid_mask_with_$B
-	${FSLDIR}/bin/avwmaths ${B}_valid_mask_with_$A -mul ${B}_talmask ${B}_valid_mask_with_$A
+    if [ "$stdroi" != "" ] ; then
+	${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_brain_mask -mul 0 -add 1 $stdroi ${A}_and_${B}_stdmask
+	${FSLDIR}/bin/flirt -in ${A}_and_${B}_stdmask -ref $A -out ${A}_stdmask -applyxfm -init ${A}_to_std_inv.mat
+	${FSLDIR}/bin/flirt -in ${A}_and_${B}_stdmask -ref $B -out ${B}_stdmask -applyxfm -init ${B}_to_std_inv.mat
+	${FSLDIR}/bin/avwmaths ${A}_valid_mask_with_$B -mul ${A}_stdmask ${A}_valid_mask_with_$B
+	${FSLDIR}/bin/avwmaths ${B}_valid_mask_with_$A -mul ${B}_stdmask ${B}_valid_mask_with_$A
     fi
 fi
 
@@ -181,18 +181,18 @@ if [ $debug = 0 ] ; then
 	${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}_stdmask.* \
+	${B}_halfwayto_${A}_stdmask.* \
 	${A}_halfwayto_${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}_stdmask.* ${B}_stdmask.* \
+	${A}_and_${B}_stdmask.* \
 	${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 \
+    /bin/rm -f ${A}_to_std_inv.mat ${B}_to_std_inv.mat ${A}_to_${B}_tmp.mat \
 	${A}_halfwayto_${B}_brain.vol ${B}_halfwayto_${A}_brain.vol \
 	${B}_to_${A}.mat_avscale
 fi

siena_cal

@@ -72,7 +72,7 @@ $FSLDIR/bin/imrm sc${input}.* \
 	${input}_halfwayto_sc${input}_brain.* \
 	${input}_halfwayto_sc${input}_brain_seg.* \
 	${input}_halfwayto_sc${input}_mask.* \
-	${input}_halfwayto_sc${input}_talmask.* \
+	${input}_halfwayto_sc${input}_stdmask.* \
 	sc${input}_halfwayto_${input}.* \
 	sc${input}_halfwayto_${input}_mask.* \
 	${input}_to_sc${input}_flow.* \

siena_diff.c

@@ -27,7 +27,7 @@ void usage()
   printf("[-c <corr>] apply self-calibrating correction factor\n");
   printf("[-e]        erode joint mask a lot instead of dilating it slightly (ie find ventricle surface)\n");
   printf("[-i]        ignore flow in z (may be good if top of brain is missing)\n");
-  printf("[-m]        apply <input1_basename>_talmask to brain edge points\n");
+  printf("[-m]        apply <input1_basename>_stdmask to brain edge points\n");
   /*  printf("[-t <n>]    ignore top n slices (may be good if top of brain is missing)\n");*/
   /*  printf("[-b <n>]    ignore bottom n slices (may be good if top of brain is missing)\n");*/
   printf("[-s <options>]  <options> to be passed to segmentation (type \"fast\" to get these)\n\n");

siena_flow2tal → siena_flow2std

 #!/bin/sh
 
-#   siena_flow2tal - warp flow image into standard space
+#   siena_flow2std - warp flow image into standard space
 #
 #   Stephen Smith, FMRIB Image Analysis Group
 #
@@ -10,7 +10,7 @@
 
 
 Usage() {
-    echo "Usage: siena_flow2tal <fileroot2> <fileroot2> [-d]"
+    echo "Usage: siena_flow2std <fileroot2> <fileroot2> [-d]"
     echo "-d : debug (don't delete intermediate files)"
     exit
 }
@@ -37,25 +37,25 @@ for opts in $@ ; do
 
 done
 
-# register to MNI152 if not already done, and create halfway2tal transform
-if [ ! -f ${A}_to_tal.mat ] ; then
+# register to MNI152 if not already done, and create halfway2std transform
+if [ ! -f ${A}_to_std.mat ] ; then
     if [ `${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
+    ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_to_std.mat
 fi
 ${FSLDIR}/bin/convert_xfm -omat ${A}_halfwayto_${B}_inv.mat -inverse ${A}_halfwayto_${B}.mat
-${FSLDIR}/bin/convert_xfm -omat ${A}_halfwayto_${B}_to_tal.mat -concat ${A}_to_tal.mat ${A}_halfwayto_${B}_inv.mat
+${FSLDIR}/bin/convert_xfm -omat ${A}_halfwayto_${B}_to_std.mat -concat ${A}_to_std.mat ${A}_halfwayto_${B}_inv.mat
 
 # dilate flow image, -> standard space -> mask with ss edge image -> blur -> remask
 ${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil ${A}_to_${B}_flow_dil
 ${FSLDIR}/bin/avwmaths ${B}_to_${A}_flow -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil ${A}_to_${B}_flow_dilback
 ${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_dil -sub ${A}_to_${B}_flow_dilback -div 2 ${A}_to_${B}_flow_dil
 /bin/rm ${A}_to_${B}_flow_dilback*
-${FSLDIR}/bin/flirt -in ${A}_to_${B}_flow_dil -ref ${FSLDIR}/etc/standard/avg152T1_brain -out ${A}_to_${B}_flow_to_tal -applyxfm -init ${A}_halfwayto_${B}_to_tal.mat
-${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_tal -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_tal
-${FSLDIR}/bin/ip ${A}_to_${B}_flow_to_tal ${A}_to_${B}_flow_to_tal 0 -s 10
-${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_tal -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_tal
+${FSLDIR}/bin/flirt -in ${A}_to_${B}_flow_dil -ref ${FSLDIR}/etc/standard/avg152T1_brain -out ${A}_to_${B}_flow_to_std -applyxfm -init ${A}_halfwayto_${B}_to_std.mat
+${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_std -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_std
+${FSLDIR}/bin/ip ${A}_to_${B}_flow_to_std ${A}_to_${B}_flow_to_std 0 -s 10
+${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_std -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_std
 
 # cleanup
 if [ $debug = 0 ] ; then

sienax

@@ -49,7 +49,7 @@ regional=0
 betopts=""
 segopts=""
 nseg=3
-talroi=""
+stdroi=""
 origin3=37 # `avwval ${FSLDIR}/etc/standard/avg152T1 origin3`
 pixdim3=2  # `avwval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
 imtype=-t1
@@ -75,14 +75,14 @@ while [ _$1 != _ ] ; do
         imtype=-t2
         shift
     elif [ $1 = -t ] ; then
-	talt=`echo $2 | sed 's/-/_/g'`
-	talt=`echo "10 k $talt $pixdim3 / $origin3 + p" | dc -`
-	talroi="$talroi -roi 0 1000000 0 1000000 0 $talt 0 1"
+	stdt=`echo $2 | sed 's/-/_/g'`
+	stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc -`
+	stdroi="$stdroi -roi 0 1000000 0 1000000 0 $stdt 0 1"
 	shift 2
     elif [ $1 = -b ] ; then
-	talb=`echo $2 | sed 's/-/_/g'`
-	talb=`echo "10 k $talb $pixdim3 / $origin3 + p" | dc -`
-	talroi="$talroi -roi 0 1000000 0 1000000 $talb 1000000 0 1"
+	stdb=`echo $2 | sed 's/-/_/g'`
+	stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc -`
+	stdroi="$stdroi -roi 0 1000000 0 1000000 $stdb 1000000 0 1"
 	shift 2
     elif [ $1 = -lm ] ; then
 	lm=$2
@@ -104,54 +104,54 @@ echo "----------  extract brain  --------------------------------------------" >
 ${FSLDIR}/bin/bet $I ${I}_brain -s $betopts >> ${I}.sienax
 
 echo ""                                                                        >> ${I}.sienax
-echo "----------  register to talairach space using brain and skull  --------" >> ${I}.sienax
+echo "----------  register to stdairach space using brain and skull  --------" >> ${I}.sienax
 echo "(do not worry about histogram warnings)"                                 >> ${I}.sienax
-${FSLDIR}/bin/pairreg ${FSLDIR}/etc/standard/avg152T1_brain ${I}_brain ${FSLDIR}/etc/standard/avg152T1_skull ${I}_brain_skull ${I}2tal.mat >> ${I}.sienax 2>&1
-${FSLDIR}/bin/avscale ${I}2tal.mat ${FSLDIR}/etc/standard/avg152T1 > ${I}2tal.avscale
-xscale=`grep Scales ${I}2tal.avscale | awk '{print $4}'`
-yscale=`grep Scales ${I}2tal.avscale | awk '{print $5}'`
-zscale=`grep Scales ${I}2tal.avscale | awk '{print $6}'`
+${FSLDIR}/bin/pairreg ${FSLDIR}/etc/standard/avg152T1_brain ${I}_brain ${FSLDIR}/etc/standard/avg152T1_skull ${I}_brain_skull ${I}2std.mat >> ${I}.sienax 2>&1
+${FSLDIR}/bin/avscale ${I}2std.mat ${FSLDIR}/etc/standard/avg152T1 > ${I}2std.avscale
+xscale=`grep Scales ${I}2std.avscale | awk '{print $4}'`
+yscale=`grep Scales ${I}2std.avscale | awk '{print $5}'`
+zscale=`grep Scales ${I}2std.avscale | awk '{print $6}'`
 vscale=`echo "10 k $xscale $yscale * $zscale * p"|dc -`
 echo "VSCALING $vscale" >> ${I}.sienax
 
 echo ""                                                                        >> ${I}.sienax
-echo "----------  mask with talairach mask  ---------------------------------" >> ${I}.sienax
-${FSLDIR}/bin/convert_xfm -inverse -omat ${I}2tal_inv.mat ${I}2tal.mat
+echo "----------  mask with std mask  ---------------------------------------" >> ${I}.sienax
+${FSLDIR}/bin/convert_xfm -inverse -omat ${I}2std_inv.mat ${I}2std.mat
 MASK=${FSLDIR}/etc/standard/avg152T1_brain_mask_dil
-if [ "$talroi" != "" ] ; then
-    ${FSLDIR}/bin/avwmaths $MASK $talroi ${I}_talmaskroi
-    MASK=${I}_talmaskroi
+if [ "$stdroi" != "" ] ; then
+    ${FSLDIR}/bin/avwmaths $MASK $stdroi ${I}_stdmaskroi
+    MASK=${I}_stdmaskroi
 fi
-${FSLDIR}/bin/flirt -in $MASK -ref ${I}_brain -out ${I}_talmask -applyxfm -init ${I}2tal_inv.mat
-${FSLDIR}/bin/avwmaths ${I}_brain -mask ${I}_talmask ${I}_talmaskbrain
+${FSLDIR}/bin/flirt -in $MASK -ref ${I}_brain -out ${I}_stdmask -applyxfm -init ${I}2std_inv.mat
+${FSLDIR}/bin/avwmaths ${I}_brain -mask ${I}_stdmask ${I}_stdmaskbrain
 
 if [ $regional = 1 ] ; then
-    ${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_strucseg_periph -ref ${I}_brain -out ${I}_talmask_segperiph -applyxfm -init ${I}2tal_inv.mat
+    ${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_strucseg_periph -ref ${I}_brain -out ${I}_stdmask_segperiph -applyxfm -init ${I}2std_inv.mat
     ${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 4.5 -bin ${I}_tmpmask
-    ${FSLDIR}/bin/flirt -in ${I}_tmpmask -ref ${I}_brain -out ${I}_talmask_segvent -applyxfm -init ${I}2tal_inv.mat
+    ${FSLDIR}/bin/flirt -in ${I}_tmpmask -ref ${I}_brain -out ${I}_stdmask_segvent -applyxfm -init ${I}2std_inv.mat
     /bin/rm ${I}_tmpmask*
 fi
 
 echo ""                                                                        >> ${I}.sienax
 echo "----------  segment tissue into types  --------------------------------" >> ${I}.sienax
 if [ $nseg = 2 ] ; then
-    ${FSLDIR}/bin/fast -c 2 $imtype -e -ov $segopts ${I}_talmaskbrain >> ${I}.sienax 2>&1
+    ${FSLDIR}/bin/fast -c 2 $imtype -e -ov $segopts ${I}_stdmaskbrain >> ${I}.sienax 2>&1
     echo "" >> ${I}.sienax
     echo "----------  convert brain volume into normalised volume  --------------" >> ${I}.sienax
-    S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_1 -m -v`
+    S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_1 -m -v`
     xa=`echo $S | awk '{print $1}'`
     xb=`echo $S | awk '{print $3}'`
     brain=`echo "2 k $xa $xb * $vscale * p" | dc -`
 else
     if [ _$lm != _ ] ; then
-	${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_talmaskbrain ${I}_talmaskbrain
+	${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_stdmaskbrain ${I}_stdmaskbrain
     fi
 
-    ${FSLDIR}/bin/fast $imtype -e -ov $segopts ${I}_talmaskbrain >> ${I}.sienax 2>&1
+    ${FSLDIR}/bin/fast $imtype -e -ov $segopts ${I}_stdmaskbrain >> ${I}.sienax 2>&1
 
     if [ _$lm != _ ] ; then
-	${FSLDIR}/bin/avwmaths_32R $lm -bin -max ${I}_talmaskbrain_pve_2 ${I}_talmaskbrain_pve_2
-	${FSLDIR}/bin/avwmaths_32SI $lm -bin -mul 3 -max ${I}_talmaskbrain_seg ${I}_talmaskbrain_seg
+	${FSLDIR}/bin/avwmaths_32R $lm -bin -max ${I}_stdmaskbrain_pve_2 ${I}_stdmaskbrain_pve_2
+	${FSLDIR}/bin/avwmaths_32SI $lm -bin -mul 3 -max ${I}_stdmaskbrain_seg ${I}_stdmaskbrain_seg
     fi
 
     echo "" >> ${I}.sienax
@@ -159,29 +159,29 @@ else
     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`
+	${FSLDIR}/bin/avwmaths_32R ${I}_stdmaskbrain_pve_1 -mas ${I}_stdmask_segperiph ${I}_stdmaskbrain_pve_1_segperiph
+	S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_1_segperiph -m -v`
 	xa=`echo $S | awk '{print $1}'`
 	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 "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`
+	${FSLDIR}/bin/avwmaths_32R ${I}_stdmaskbrain_pve_0 -mas ${I}_stdmask_segvent ${I}_stdmaskbrain_pve_0_segvent
+	S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_0_segvent -m -v`
 	xa=`echo $S | awk '{print $1}'`
 	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 "vcsf               $xg $uxg (ventricular CSF)" >> ${I}.sienax
     fi
-    S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_1 -m -v`
+    S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_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 "GREY               $ngrey $ugrey" >> ${I}.sienax
-    S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_2 -m -v`
+    S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_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 -`
@@ -193,16 +193,16 @@ ubrain=`echo "2 k $uwhite $ugrey + 1 / p" | dc -`
 nbrain=`echo "2 k $nwhite $ngrey + 1 / p" | dc -`
 echo "BRAIN              $nbrain $ubrain" >> ${I}.sienax
 
-${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_talmaskbrain_seg 1.9 5 ${I}_render
+${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_stdmaskbrain_seg 1.9 5 ${I}_render
 
 if [ $regional = 1 ] ; then
-    ${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_talmaskbrain_pve_1_segperiph 0.3 0.7 ${I}_periph_render
-    ${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_talmaskbrain_pve_0_segvent   0.3 0.7 ${I}_vent_render
+    ${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_stdmaskbrain_pve_1_segperiph 0.3 0.7 ${I}_periph_render
+    ${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_stdmaskbrain_pve_0_segvent   0.3 0.7 ${I}_vent_render
 fi
 
 if [ $debug = 0 ] ; then
-    /bin/rm -f `$FSLDIR/bin/imglob ${I}_brain* ${I}_talmask*`
-    /bin/rm -f ${I}2tal.avscale ${I}2tal_inv.mat
+    /bin/rm -f `$FSLDIR/bin/imglob ${I}_brain* ${I}_stdmask*`
+    /bin/rm -f ${I}2std.avscale ${I}2std_inv.mat
 fi
 
 echo "$nbrain"