From 219c944c7940c914f9f67e5a0f1ede3545f57d7b Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Mon, 20 Feb 2006 12:04:45 +0000
Subject: [PATCH] CVS:
----------------------------------------------------------------------
---
Makefile | 4 +-
doc/index.html | 8 ++--
lesions_0.1 | 6 +--
lesions_0.2 | 6 +--
lesions_0.3 | 6 +--
siena | 70 ++++++++++++++--------------
siena_cal | 2 +-
siena_diff.c | 2 +-
siena_flow2tal => siena_flow2std | 20 ++++----
sienax | 78 ++++++++++++++++----------------
10 files changed, 102 insertions(+), 100 deletions(-)
rename siena_flow2tal => siena_flow2std (66%)
diff --git a/Makefile b/Makefile
index a454d9b..8b59d6f 100644
--- a/Makefile
+++ b/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} ${LIBCC}
diff --git a/doc/index.html b/doc/index.html
index c3a2ba0..1191c06 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -463,7 +463,7 @@ significantly with age or disease progression.
<LI> Run <br><code>siena A B</code><br> on all subjects'
two-timepoints data (here <code>A</code> and <code>B</code>).
-<LI> For each subject run <br><code>siena_flow2tal A B</code><br> -
+<LI> For each subject run <br><code>siena_flow2std A B</code><br> -
this runs flirt to generate the transform to standard space (if it
doesn't already exist), takes the edge flow (atrophy) image generated
by <code>siena</code>, dilates this several times (to "thicken" this edge
@@ -471,15 +471,15 @@ flow image), transforms to standard space, and masks with a standard
space edge mask. It then smooths this with a Gaussian filter of
half-width 10mm before remasking; you may want to edit this or even
remove this step - find the call to <code>ip</code> in
-$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
diff --git a/lesions_0.1 b/lesions_0.1
index fa88ede..fd0e70b 100755
--- a/lesions_0.1
+++ b/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
diff --git a/lesions_0.2 b/lesions_0.2
index af2f7af..a2c204c 100755
--- a/lesions_0.2
+++ b/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
diff --git a/lesions_0.3 b/lesions_0.3
index 865209c..6273f26 100644
--- a/lesions_0.3
+++ b/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
diff --git a/siena b/siena
index b37dd38..f4e9b49 100755
--- a/siena
+++ b/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
diff --git a/siena_cal b/siena_cal
index 71eb4d2..2b62cf9 100755
--- a/siena_cal
+++ b/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.* \
diff --git a/siena_diff.c b/siena_diff.c
index db3b36e..3176c42 100644
--- a/siena_diff.c
+++ b/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");
diff --git a/siena_flow2tal b/siena_flow2std
similarity index 66%
rename from siena_flow2tal
rename to siena_flow2std
index 0296d4b..6ed198c 100755
--- a/siena_flow2tal
+++ b/siena_flow2std
@@ -1,6 +1,6 @@
#!/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
diff --git a/sienax b/sienax
index 223b69b..01e737f 100755
--- a/sienax
+++ b/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"
--
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