From 7b81cf5b3ad3d3c0111b2dbd9ba180d25a2b8c9b Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Thu, 16 Feb 2006 09:39:14 +0000
Subject: [PATCH] removed reference to Talairach
---
doc/index.html | 16 ++++++++--------
siena | 14 +++++++-------
sienax | 4 ++--
3 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/doc/index.html b/doc/index.html
index ceabe0d..c3a2ba0 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -37,7 +37,7 @@ voxelwise statistical testing.
image, normalised for skull size. It calls a series of FSL programs:
It first strips non-brain tissue, and then uses the brain and skull
images to estimate the scaling between the subject's image and
-Talairach space. It then runs tissue segmentation to estimate the
+standard space. It then runs tissue segmentation to estimate the
volume of brain tissue, and multiplies this by the estimated scaling
factor, to reduce head-size-related variability between subjects.
@@ -213,17 +213,17 @@ matter separately) - use this if there is poor grey/white contrast
<p><b>-t2</b>: tell FAST that the input images are T2-weighted and not T1
-<p><b>-m</b> : use Talairach-space masking as well as BET (e.g. if it
+<p><b>-m</b> : use standard-space masking as well as BET (e.g. if it
is proving hard to get reliable brain segmentation from BET, for
-example if eyes are hard to segment out) - register to Talairach space
-in order to use a pre-defined Talairach-space brain mask
+example if eyes are hard to segment out) - register to standard space
+in order to use a pre-defined standard-space brain mask
-<p><b>-t <t></b>: ignore from t (mm) upwards in Talairach space
+<p><b>-t <t></b>: ignore from t (mm) upwards in MNI152/Talairach space
- if you need to ignore the top part of the head (e.g. if some
subjects have the top missing and you need consistency across
subjects)
-<p><b>-b <b></b>: ignore from b (mm) downwards in Talairach space; b should probably be -ve
+<p><b>-b <b></b>: ignore from b (mm) downwards in MNI152/Talairach space; b should probably be -ve
<p><b>-S "siena_diff options"</b> : if you want to send options to the
siena_diff program (that estimates change between two aligned
@@ -360,12 +360,12 @@ matter separately) - use this if there is poor grey/white contrast
<p><b>-t2</b>: tell FAST that the input images are T2-weighted and not T1
-<p><b>-t <t></b>: ignore from t (mm) upwards in Talairach space
+<p><b>-t <t></b>: ignore from t (mm) upwards in MNI152/Talairach space
- if you need to ignore the top part of the head (e.g. if some
subjects have the top missing and you need consistency across
subjects)
-<p><b>-b <b></b>: ignore from b (mm) downwards in Talairach space; b should probably be -ve
+<p><b>-b <b></b>: ignore from b (mm) downwards in MNI152/Talairach space; b should probably be -ve
<p><b>-r</b>: tell SIENAX to estimate "regional" volumes as well as
global; this produces peripheral cortex GM volume (3-class
diff --git a/siena b/siena
index a9fe953..d1776fd 100755
--- a/siena
+++ b/siena
@@ -16,9 +16,9 @@ Usage() {
echo "-B \"betopts\" : options to pass to BET brain extraction (inside double-quotes), e.g. -B \"-f 0.3\""
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 "-m : use standard-space masking as well as BET"
+ echo "-t <t> : ignore from t (mm) upwards in MNI152/Talairach space"
+ echo "-b <b> : ignore from b (mm) downwards in MNI152/Talairach space; b should probably be -ve"
echo "-S \"sienadiffopts\" : options to pass to siena_diff timepoint differencing (inside double-quotes), e.g. -S \"-s -i 20\""
echo ""
exit
@@ -124,7 +124,7 @@ ${FSLDIR}/bin/avwmaths ${B}_valid_mask -mul ${A}_valid_mask_to_${B} ${B}_valid_m
if [ $dotal = 1 ] ; then
echo "" >> ${A}_to_${B}.siena
- echo "---------- Talairach space masking ----------------------------------" >> ${A}_to_${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 -matonly -inverse -omat ${A}_to_tal_inv.mat ${A}_to_tal.mat
@@ -132,10 +132,10 @@ if [ $dotal = 1 ] ; then
${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
+ echo "rmsdiff for standard space transform 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
+ echo "Warning! Probably failed consistency check for standard-space registrations!"
+ echo "Warning! Probably failed consistency check for standard-space registrations!" >> ${A}_to_${B}.siena
fi
if [ $talmask = 1 ] ; then
diff --git a/sienax b/sienax
index 7eff770..01075ee 100755
--- a/sienax
+++ b/sienax
@@ -16,8 +16,8 @@ Usage() {
echo "-B \"betopts\" : options to pass to BET brain extraction (inside double-quotes), e.g. -B \"-f 0.3\""
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 "-t <t> : ignore from t (mm) upwards in MNI152/Talairach space"
+ echo "-b <b> : ignore from b (mm) downwards in MNI152/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 "-S \"segopts\" : options to pass to FAST segmentation (inside double-quotes), e.g. -S \"-i 20\""
--
GitLab