removed reference to Talairach

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 &lt;t&gt;</b>: ignore from t (mm) upwards in Talairach space
+<p><b>-t &lt;t&gt;</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 &lt;b&gt;</b>: ignore from b (mm) downwards in Talairach space; b should probably be -ve
+<p><b>-b &lt;b&gt;</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 &lt;t&gt;</b>: ignore from t (mm) upwards in Talairach space
+<p><b>-t &lt;t&gt;</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 &lt;b&gt;</b>: ignore from b (mm) downwards in Talairach space; b should probably be -ve
+<p><b>-b &lt;b&gt;</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

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

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\""