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@@ -4,16 +4,19 @@
<TITLE>SIENA - Structural Brain Change Analysis</TITLE>
</HEAD><BODY BACKGROUND="../images/fsl-bg.jpg">
<hr><TABLE BORDER=0 WIDTH="100%"><TR>
-<TD ALIGN=CENTER><H1>SIENA Structural Brain Change Analysis<br>User
-Guide<br></H1>(SIENA - Structural Image Evaluation, using
-Normalisation, of Atrophy - Version 2.2)
+<TD ALIGN=CENTER><H1>SIENA Structural Brain Change Analysis</H1>
+SIENA - Structural Image Evaluation, using Normalisation, of Atrophy - Version 2.3<br><br>
+
+<a href="#intro">intro</a> - <a href="#tools">tools used</a> - <a href="#siena">SIENA</a> - <a
+href="#sienax">SIENAX</a> - <a href="#sienar">voxelwise SIENA statistics</a>
+
<TD ALIGN=RIGHT><a href="../index.html"><IMG BORDER=0 SRC="../images/fsl-logo.jpg"></a>
</TR></TABLE>
<!-- }}} -->
<!-- {{{ Introduction -->
-<hr><H2>Introduction</H2>
+<a name="intro"></a><p><hr><H2>Introduction</H2>
<p>SIENA is a package for both single-time-point ("cross-sectional")
and two-time-point ("longitudinal") analysis of brain change, in
@@ -50,7 +53,7 @@ references listed there.
<!-- }}} -->
<!-- {{{ FSL Tools used -->
-<hr><H2>FSL Tools used</H2>
+<a name="tools"></a><p><hr><H2>FSL Tools used</H2>
This section lists the generic FSL programs that SIENA uses.
@@ -83,9 +86,9 @@ important to choose the right option here, depending on whether there
is or is not reasonable grey-white contrast in the image.
<!-- }}} -->
-<!-- {{{ Two-Time-Point Estimation -->
+<!-- {{{ SIENA - Two-Time-Point Estimation -->
-<hr><H2>Two-Time-Point Estimation</H2>
+<a name="siena"></a><p><hr><H2>SIENA - Two-Time-Point Estimation</H2>
<h3>Usage</h3>
@@ -94,9 +97,9 @@ href="siena_usage">usage</a>) is run simply by typing
<p><b>siena <input1_fileroot> <input2_fileroot></b>
-<p>where the two input fileroots are analyze images without the .hdr
-or .img extensions. Note that the input fileroot must not contain
-directory names - i.e. all must be done within a single directory.
+<p>where the two input fileroots are images without any filename
+extensions. Note that the input fileroot must not contain directory
+names - i.e. all must be done within a single directory.
<p>Other options are:
@@ -109,6 +112,8 @@ and vice versa
<p><b>-2</b> : two-class segmentation (don't segment grey and white
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
is proving hard to get reliable brain segmentation from BET, for
example if eyes are hard to segment out) - register to Talairach space
@@ -200,7 +205,7 @@ images are called "A" and "B"):
<LI>A_to_B.siena the output information from the <b>siena</b> script.
-<LI>A_halfwayto_B_render.hdr a colour rendered image of edge motion
+<LI>A_halfwayto_B_render a colour rendered image of edge motion
superimposed on the halfway A image.
<LI>B_regto_A.gif a gif image showing the results of the registration,
@@ -219,9 +224,9 @@ the images to the halfway positions.
</UL>
<!-- }}} -->
-<!-- {{{ Single-Time-Point Estimation -->
+<!-- {{{ SIENAX - Single-Time-Point Estimation -->
-<hr><H2>Single-Time-Point Estimation</H2>
+<a name="sienax"></a><p><hr><H2>SIENAX - Single-Time-Point Estimation</H2>
<h3>Usage</h3>
@@ -230,9 +235,9 @@ href="sienax_usage">usage</a>) is run simply by typing
<p><b>sienax <input_fileroot></b>
-<p>where the input fileroot is an analyze image without the .hdr or
-.img extension. Note that the input fileroot must not contain
-directory names - i.e. all must be done within a single directory.
+<p>where the input fileroot is an image without any filename
+extension. Note that the input fileroot must not contain directory
+names - i.e. all must be done within a single directory.
<p>Other options are:
@@ -246,6 +251,8 @@ and vice versa
<p><b>-2</b> : two-class segmentation (don't segment grey and white
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
- 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
@@ -253,6 +260,12 @@ subjects)
<p><b>-b <b></b>: ignore from b (mm) downwards in Talairach space; b should probably be -ve
+<p><b>-r</b>: tell FAST to estimate "regional" volumes as well as
+global; this produces peripheral cortex GM volume (3-class
+segmentation only) and ventricular CSF volume
+
+<p><b>-lm <mask></b>: use a lesion (or lesion+CSF) mask to
+remove incorrectly labelled "grey matter" voxels
<h3>What the script does</h3>
@@ -311,12 +324,40 @@ image is called "A"):
<LI>A.sienax the output information from the <b>sienax</b> script.
-<LI>A_render.hdr a colour rendered image showing the segmentation
+<LI>A_render a colour rendered image showing the segmentation
output superimposed on top of the original image.
<LI>A2tal.mat the transformation that takes the input image into
standard space.
+</UL>
+
+<!-- }}} -->
+<!-- {{{ Voxelwise SIENA Statistics -->
+
+<a name="sienar"></a><p><hr><H2>Voxelwise SIENA Statistics</H2>
+
+<p>We have recently extended SIENA to allow the voxelwise statistical
+analysis of atrophy across subjects. This takes a SIENA-derived edge
+flow image for each subject, warps these to align with a
+standard-space edge image and then carries out voxelwise cross-subject
+statistical analysis to identify brain edge points which, for example,
+are signficantly atrophic for the group of subjects as a whole, or
+where atrophy correlates significantly with age or disease
+progression.
+
+<p>In order to carry out voxelwise SIENA statistics, do the following:
+
+<UL>
+
+<LI> Run <b>siena <A>: <B>:</b> on all subjects.
+
+<LI>
+
+
+
+
+
</UL>
<!-- }}} -->
@@ -383,7 +424,7 @@ standard space.
<!-- }}} -->
<!-- {{{ end -->
-<p><HR><FONT SIZE=1>Copyright © 2000, University of
+<p><HR><FONT SIZE=1>Copyright © 2000-2004, University of
Oxford. Written by <A
HREF="http://www.fmrib.ox.ac.uk/~steve/index.html">S. Smith</A>.</FONT>