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<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 &lt;input1_fileroot&gt; &lt;input2_fileroot&gt;</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 &lt;input_fileroot&gt;</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 &lt;t&gt;</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 &lt;b&gt;</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 &lt;mask&gt;</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 &lt;A&gt: &lt;B&gt:</b> on all subjects.
<LI>
</UL>
<!-- }}} -->
......@@ -383,7 +424,7 @@ standard space.
<!-- }}} -->
<!-- {{{ end -->
<p><HR><FONT SIZE=1>Copyright &copy; 2000, University of
<p><HR><FONT SIZE=1>Copyright &copy; 2000-2004, University of
Oxford. Written by <A
HREF="http://www.fmrib.ox.ac.uk/~steve/index.html">S. Smith</A>.</FONT>
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