diff --git a/doc/index.html b/doc/index.html
index d4e7d914bf068f48d014cf464d62239e189a168d..505208dba3bc9af00251a124b3cd91125fff69c4 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -350,7 +350,7 @@ progression.
<UL>
-<LI> Run <b>siena <A>: <B>:</b> on all subjects.
+<LI> Run <b>siena <A> <B></b> on all subjects.
<LI>
diff --git a/doc/siena b/doc/siena
deleted file mode 100755
index ec68a13a790761a79456e82ef09d091d8ff10324..0000000000000000000000000000000000000000
--- a/doc/siena
+++ /dev/null
@@ -1,206 +0,0 @@
-#!/bin/sh
-
-# siena - Structural Image Evaluation, including Normalisation, of Atrophy
-#
-# Stephen Smith, FMRIB Image Analysis Group
-#
-# Copyright (C) 1999-2004 University of Oxford
-#
-# SHCOPYRIGHT
-
-Usage() {
- echo ""
- echo "Usage: siena <input1_fileroot> <input2_fileroot> [-d] [-f <BET threshold>] [-2] [-t2] [-m] [-t <t>] [-b <b>] [siena_diff options]"
- echo ""
- echo "-d : debug (don't delete intermediate files)"
- echo "-f <f> : Threshold for BET brain extraction (default 0.5)"
- echo "-2 : two-class segmentation (don't segment grey and white matter separately)"
- echo "-t2 : T2-weighted input image (default T1-weighted)"
- echo "-m : use Talairach-space masking as well as BET"
- echo "-t <t> : ignore from t (mm) upwards in Talairach space"
- echo "-b <b> : ignore from b (mm) downwards in Talairach space; b should probably be -ve"
- echo ""
- exit
-}
-
-if [ _$FSLDIR = _ ] ; then
- FSLDIR=/usr/local/fsl
- export FSLDIR
-fi
-
-[ "$2" = "" ] && Usage
-[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
-[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
-A=`${FSLDIR}/bin/remove_ext $1`
-B=`${FSLDIR}/bin/remove_ext $2`
-
-echo "-----------------------------------------------------------------------" > ${A}_to_${B}.siena
-echo "" >> ${A}_to_${B}.siena
-echo " SIENA - Structural Image Evaluation, using Normalisation, of Atrophy" >> ${A}_to_${B}.siena
-echo " part of FSL www.fmrib.ox.ac.uk/fsl" >> ${A}_to_${B}.siena
-echo " running longitudinal atrophy measurement: siena version 2.2" >> ${A}_to_${B}.siena
-echo " siena $@" >> ${A}_to_${B}.siena
-echo "" >> ${A}_to_${B}.siena
-
-shift 2
-
-
-debug=0
-betf=0.5
-sdo="-m"
-dotal=0
-talmask=0
-talroi=""
-origin3=37 # `avwval ${FSLDIR}/etc/standard/avg152T1 origin3`
-pixdim3=2 # `avwval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
-
-for opts in $@ ; do
-
- if [ $opts = -d ] ; then
- debug=1
- ov=-ov
- shift
- fi
-
- if [ $opts = -f ] ; then
- betf=$2
- shift 2
- fi
-
- if [ $opts = -2 ] ; then
- sdo="$sdo -2"
- shift
- fi
-
- if [ $opts = -t2 ] ; then
- is_t2=" -s -t2"
- shift
- fi
-
- if [ $opts = -m ] ; then
- talmask=1
- dotal=1
- shift
- fi
-
- if [ $opts = -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"
- shift 2
- fi
-
- if [ $opts = -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 $talb 1000000 0 1"
- shift 2
- fi
-
-done
-
-sdo="${sdo}${is_t2}"
-
-echo "---------- extract brain --------------------------------------------" >> ${A}_to_${B}.siena
-${FSLDIR}/bin/bet $A ${A}_brain -s -m -f $betf >> ${A}_to_${B}.siena
-${FSLDIR}/bin/bet $B ${B}_brain -s -m -f $betf >> ${A}_to_${B}.siena
-
-echo "" >> ${A}_to_${B}.siena
-echo "---------- register brains and skulls -------------------------------" >> ${A}_to_${B}.siena
-echo "(do not worry about histogram warnings)" >> ${A}_to_${B}.siena
-${FSLDIR}/bin/siena_flirt $A $B >> ${A}_to_${B}.siena 2>&1
-
-echo "" >> ${A}_to_${B}.siena
-echo "---------- produce valid masks --------------------------------------" >> ${A}_to_${B}.siena
-XDIM=`${FSLDIR}/bin/avwval $A dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
-YDIM=`${FSLDIR}/bin/avwval $A dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
-ZDIM=`${FSLDIR}/bin/avwval $A dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
-${FSLDIR}/bin/avwmaths ${A}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${A}_valid_mask
-XDIM=`${FSLDIR}/bin/avwval $B dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
-YDIM=`${FSLDIR}/bin/avwval $B dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
-ZDIM=`${FSLDIR}/bin/avwval $B dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
-${FSLDIR}/bin/avwmaths ${B}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${B}_valid_mask
-${FSLDIR}/bin/flirt -in ${B}_valid_mask -ref $A -out ${B}_valid_mask_to_${A} -applyxfm -init ${B}_to_${A}.mat -paddingsize 0
-${FSLDIR}/bin/flirt -in ${A}_valid_mask -ref $B -out ${A}_valid_mask_to_${B} -applyxfm -init ${A}_to_${B}.mat -paddingsize 0
-${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
- echo "" >> ${A}_to_${B}.siena
- echo "---------- Talairach 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 -matonly -inverse -omat ${A}_to_tal_inv.mat ${A}_to_tal.mat
- ${FSLDIR}/bin/convert_xfm -matonly -inverse -omat ${B}_to_tal_inv.mat ${B}_to_tal.mat
-
- ${FSLDIR}/bin/convert_xfm -matonly -concat ${B}_to_tal_inv.mat -omat ${A}_to_${B}_tmp.mat ${A}_to_tal.mat
- RMSDIFF=`${FSLDIR}/bin/rmsdiff ${A}_to_${B}.mat ${A}_to_${B}_tmp.mat $A | sed 's/\..*$/ /g'` # last part makes it integer
- echo "rmsdiff for Talairaching is $RMSDIFF mm" >> ${A}_to_${B}.siena
- if [ $RMSDIFF -ge 10 ] ; then
- echo "Warning! Probably failed consistency check for Talairach registrations!"
- echo "Warning! Probably failed consistency check for Talairach 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 ${B}_brain_mask
- fi
-
- if [ "$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
- fi
-fi
-
-echo "" >> ${A}_to_${B}.siena
-echo "---------- change analysis ------------------------------------------" >> ${A}_to_${B}.siena
-corr1=`${FSLDIR}/bin/siena_cal $A $B 1.002 $sdo $@`
-corr2=`${FSLDIR}/bin/siena_cal $B $A 1.002 $sdo $@`
-corr=`echo "10 k $corr1 $corr2 + 2.0 / p" | dc -`
-echo "corr1=$corr1 corr2=$corr2 corr=$corr" >> ${A}_to_${B}.siena
-
-echo "" >> ${A}_to_${B}.siena
-${FSLDIR}/bin/siena_diff ${B} ${A} -c $corr $sdo $@ >> ${A}_to_${B}.siena
-pbvc_backward=`grep PBVC ${A}_to_${B}.siena | tail -1 | awk '{print $2}' | sed 's/-/_/g'`
-
-echo "" >> ${A}_to_${B}.siena
-${FSLDIR}/bin/siena_diff ${A} ${B} -c $corr $sdo $@ >> ${A}_to_${B}.siena
-pbvc_forward=`grep PBVC ${A}_to_${B}.siena | tail -1 | awk '{print $2}' | sed 's/-/_/g'`
-
-echo "" >> ${A}_to_${B}.siena
-pbvc_average=`echo "10 k $pbvc_forward $pbvc_backward - 2.0 / p" | dc -`
-echo "finalPBVC $pbvc_average %" >> ${A}_to_${B}.siena
-
-${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
- $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/siena_usage b/doc/siena_usage
deleted file mode 100755
index 76d8a1590e54e146e972f854769cd2aa0ea3653c..0000000000000000000000000000000000000000
--- a/doc/siena_usage
+++ /dev/null
@@ -1,11 +0,0 @@
-
-Usage: siena <input1_fileroot> <input2_fileroot> [-d] [-f <BET threshold>] [-2] [-t2] [-m] [-t <t>] [-b <b>] [siena_diff options]
-
--d : debug (don't delete intermediate files)
--f <f> : Threshold for BET brain extraction (default 0.5)
--2 : two-class segmentation (don't segment grey and white matter separately)
--t2 : T2-weighted input image (default T1-weighted)
--m : use Talairach-space masking as well as BET
--t <t> : ignore from t (mm) upwards in Talairach space
--b <b> : ignore from b (mm) downwards in Talairach space; b should probably be -ve
-
diff --git a/doc/sienax b/doc/sienax
deleted file mode 100755
index cec4b3dabb29dcd40675798a351cb494a93e60db..0000000000000000000000000000000000000000
--- a/doc/sienax
+++ /dev/null
@@ -1,209 +0,0 @@
-#!/bin/sh
-
-# sienax - Structural Image Evaluation, including Normalisation, of Atrophy (X-sectional)
-#
-# Stephen Smith, FMRIB Image Analysis Group
-#
-# Copyright (C) 1999-2004 University of Oxford
-#
-# SHCOPYRIGHT
-
-Usage() {
- echo ""
- echo "Usage: sienax <input_fileroot> [-d] [-f <BET threshold>] [-2] [-t2] [-t <t>] [-b <b>] [-r] [-lm <lesion_mask>] [segmentation options]"
- echo ""
- echo "-d : debug (don't delete intermediate files)"
- echo "-f <f> : Threshold for BET brain extraction (default f=0.5)"
- echo "-2 : two-class segmentation (don't segment grey and white matter separately)"
- echo "-t2 : T2-weighted input image (default T1-weighted)"
- echo "-t <t> : ignore from t (mm) upwards in Talairach space"
- echo "-b <b> : ignore from b (mm) downwards in Talairach space. b should probably be -ve"
- echo "-r : regional - use standard-space masks to give peripheral cortex GM volume (3-class segmentation only) and ventricular CSF volume"
- echo "-lm <mask> : use lesion (or lesion+CSF) mask to remove incorrectly labelled \"grey matter\" voxels"
- echo ""
- exit
-}
-
-if [ _$FSLDIR = _ ] ; then
- FSLDIR=/usr/local/fsl
- export FSLDIR
-fi
-
-[ _$1 = _ ] && Usage
-I=`${FSLDIR}/bin/remove_ext $1`;
-[ `${FSLDIR}/bin/imtest $I` = 0 ] && Usage
-
-echo "-----------------------------------------------------------------------" > ${I}.sienax
-echo "" >> ${I}.sienax
-echo " SIENA - Structural Image Evaluation, using Normalisation, of Atrophy" >> ${I}.sienax
-echo " part of FSL www.fmrib.ox.ac.uk/fsl" >> ${I}.sienax
-echo " running cross-sectional atrophy measurement: sienax version 2.2" >> ${I}.sienax
-echo " sienax $@" >> ${I}.sienax
-echo "" >> ${I}.sienax
-
-shift
-
-debug=0
-regional=0
-betf=0.5
-nseg=3
-talroi=""
-origin3=37 # `avwval ${FSLDIR}/etc/standard/avg152T1 origin3`
-pixdim3=2 # `avwval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
-imtype=-t1
-
-for opts in $@ ; do
-
- if [ $opts = -d ] ; then
- debug=1
- shift
- fi
-
- if [ $opts = -r ] ; then
- regional=1
- shift
- fi
-
- if [ $opts = -f ] ; then
- betf=$2
- shift 2
- fi
-
- if [ $opts = -2 ] ; then
- nseg=2
- shift
- fi
-
- if [ $opts = -t2 ] ; then
- imtype=-t2
- shift
- fi
-
- if [ $opts = -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"
- shift 2
- fi
-
- if [ $opts = -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"
- shift 2
- fi
-
- if [ $opts = -lm ] ; then
- lm=$2
- shift 2
- fi
-
-done
-
-if [ $regional = 1 ] ; then
- if [ $nseg = 2 ] ; then
- echo "Can't do regional analysis with 2-class segmentation"
- exit
- fi
-fi
-
-echo "---------- extract brain --------------------------------------------" >> ${I}.sienax
-${FSLDIR}/bin/bet $I ${I}_brain -s -f $betf >> ${I}.sienax
-
-echo "" >> ${I}.sienax
-echo "---------- register to talairach 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}'`
-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 -matonly -inverse -omat ${I}2tal_inv.mat ${I}2tal.mat
-MASK=${FSLDIR}/etc/standard/avg152T1_brain_mask_dil
-if [ "$talroi" != "" ] ; then
- ${FSLDIR}/bin/avwmaths $MASK $talroi ${I}_talmaskroi
- MASK=${I}_talmaskroi
-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
-
-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/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
- /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 $@ ${I}_talmaskbrain >> ${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`
- xa=`echo $S | awk '{print $1}'`
- xb=`echo $S | awk '{print $3}'`
- brain=`echo "2 k $xa $xb * $vscale * p" | dc -`
-else
- ${FSLDIR}/bin/fast $imtype -e -ov $@ ${I}_talmaskbrain >> ${I}.sienax 2>&1
-
- if [ _$lm != _ ] ; then
- ${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_talmaskbrain_pve_1 ${I}_talmaskbrain_pve_1
- fi
-
- echo "" >> ${I}.sienax
- echo "---------- convert brain volume into normalised 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`
- xa=`echo $S | awk '{print $1}'`
- xb=`echo $S | awk '{print $3}'`
- xg=`echo "2 k $xa $xb * $vscale * p" | dc -`
- echo "" >> ${I}.sienax
- echo "pgrey $xg" >> ${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`
- xa=`echo $S | awk '{print $1}'`
- xb=`echo $S | awk '{print $3}'`
- xg=`echo "2 k $xa $xb * $vscale * p" | dc -`
- echo "" >> ${I}.sienax
- echo "vcsf $xg" >> ${I}.sienax
- fi
- S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_1 -m -v`
- xa=`echo $S | awk '{print $1}'`
- xb=`echo $S | awk '{print $3}'`
- grey=`echo "2 k $xa $xb * $vscale * p" | dc -`
- S=`${FSLDIR}/bin/avwstats ${I}_talmaskbrain_pve_2 -m -v`
- xa=`echo $S | awk '{print $1}'`
- xb=`echo $S | awk '{print $3}'`
- white=`echo "2 k $xa $xb * $vscale * p" | dc -`
- brain=`echo "2 k $white $grey + p" | dc -`
- echo "" >> ${I}.sienax
- echo "GREY $grey" >> ${I}.sienax
- echo "WHITE $white" >> ${I}.sienax
-fi
-
-echo "" >> ${I}.sienax
-echo "BRAIN $brain" >> ${I}.sienax
-echo "" >> ${I}.sienax
-
-${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_talmaskbrain_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
-fi
-
-if [ $debug = 0 ] ; then
- /bin/rm -f `$FSLDIR/bin/imglob ${I}_brain* ${I}_talmask*`
- /bin/rm -f ${I}2tal.avscale ${I}2tal_inv.mat
-fi
-
-echo "$brain"
-
diff --git a/doc/sienax_usage b/doc/sienax_usage
deleted file mode 100755
index 8c2c12c7042d63aa1e94bf9c433c5b28538ca2c9..0000000000000000000000000000000000000000
--- a/doc/sienax_usage
+++ /dev/null
@@ -1,12 +0,0 @@
-
-Usage: sienax <input_fileroot> [-d] [-f <BET threshold>] [-2] [-t2] [-t <t>] [-b <b>] [-r] [-lm <lesion_mask>] [segmentation options]
-
--d : debug (don't delete intermediate files)
--f <f> : Threshold for BET brain extraction (default f=0.5)
--2 : two-class segmentation (don't segment grey and white matter separately)
--t2 : T2-weighted input image (default T1-weighted)
--t <t> : ignore from t (mm) upwards in Talairach space
--b <b> : ignore from b (mm) downwards in Talairach space. b should probably be -ve
--r : regional - use standard-space masks to give peripheral cortex GM volume (3-class segmentation only) and ventricular CSF volume
--lm <mask> : use lesion (or lesion+CSF) mask to remove incorrectly labelled "grey matter" voxels
-
diff --git a/siena b/siena
index ec68a13a790761a79456e82ef09d091d8ff10324..36bd5f4c3712b3d141cdb371dcf41ca5c6fad128 100755
--- a/siena
+++ b/siena
@@ -38,7 +38,7 @@ echo "-----------------------------------------------------------------------" >
echo "" >> ${A}_to_${B}.siena
echo " SIENA - Structural Image Evaluation, using Normalisation, of Atrophy" >> ${A}_to_${B}.siena
echo " part of FSL www.fmrib.ox.ac.uk/fsl" >> ${A}_to_${B}.siena
-echo " running longitudinal atrophy measurement: siena version 2.2" >> ${A}_to_${B}.siena
+echo " running longitudinal atrophy measurement: siena version 2.3" >> ${A}_to_${B}.siena
echo " siena $@" >> ${A}_to_${B}.siena
echo "" >> ${A}_to_${B}.siena
diff --git a/sienax b/sienax
index cec4b3dabb29dcd40675798a351cb494a93e60db..e95e5e52ab5e45730bd3b3619e81d09bc24bca8b 100755
--- a/sienax
+++ b/sienax
@@ -37,7 +37,7 @@ echo "-----------------------------------------------------------------------" >
echo "" >> ${I}.sienax
echo " SIENA - Structural Image Evaluation, using Normalisation, of Atrophy" >> ${I}.sienax
echo " part of FSL www.fmrib.ox.ac.uk/fsl" >> ${I}.sienax
-echo " running cross-sectional atrophy measurement: sienax version 2.2" >> ${I}.sienax
+echo " running cross-sectional atrophy measurement: sienax version 2.3" >> ${I}.sienax
echo " sienax $@" >> ${I}.sienax
echo "" >> ${I}.sienax