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<TITLE>BET - Brain Extraction Tool</TITLE>
</HEAD><BODY BACKGROUND="../images/fsl-bg.jpg">
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<TD ALIGN=CENTER><H1>BET - Brain Extraction Tool - User Guide</H1>BET Version 1.2
<TD ALIGN=RIGHT><a href="../index.html"><IMG BORDER=0 SRC="../images/fsl-logo.jpg"></a>
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<HR><H2>INTRODUCTION</H2>
 
<P>BET (Brain Extraction Tool) deletes non-brain tissue from an
image of the whole head. It can also estimate the external skull
surface.

<P>For more detail on BET and an updated journal reference, see the <A
HREF="http://www.fmrib.ox.ac.uk/analysis/research/bet/">BET research
web page</A>. If you use BET in your research, please quote the
journal reference listed there.

<p>The different BET programs are:
<UL>
<LI><a href="#Bet">Bet</a> - BET GUI<br>
<LI><a href="#bet">bet</a> - command-line BET program<br>
<LI><a href="#betfunc">betfunc</a> - command-line script using bet to
process 4D FMRI data
<LI><a href="#betpremask">betpremask</a> - command-line script to
carry out brain masking using FLIRT registration and a standard-space
mask, instead of BET
</UL>

<A NAME="Bet"></A><hr><H2>Bet GUI</H2>

<H3>MAIN OPTIONS</H3>
 
<P>By default the only output from BET is an image with all non-brain
matter removed - this is the <B>Generate image with non-brain matter
removed</B> option.

<p>The other main optional output from BET is controlled by the
<B>Generate image with estimated brain surface overlaid on
original</B> option; this output does not remove any of the original
image, but instead draws the outline of the brain's surface onto the
original image.

<H3>ADVANCED OPTIONS</H3>
 
<H3>Other optional outputs</H3>
  
<P>The <B>Generate binary brain mask image</B> option tells BET to
output a binary brain mask (0 outside of the brain and 1 inside). This
can then be used in later processing, to mask other images derived
from the original.

<P>The <B>Apply thresholding to segmented brain image (and mask if
required)</B> option causes BET to apply thresholding to the segmented
brain image (and also the brain mask if selected). Thus, inside the
estimated brain, some voxels can be "zeroed" after segmentation, if
their intensity falls below an automatically estimated threshold.

<P>The <B>Generate exterior skull surface image</B> option tells BET
to produce an image which is an estimate of the exterior surface of
the skull. All non-skull-surface points are 0 in this image, and
skull-surface points are 100.

<H3>User-settable thresholds</H3>
 
<P>Changing <B>Fractional intensity threshold</B> from its default
value of 0.5 will cause the overall segmented brain to become larger
(<0.5) or smaller (>0.5). This threshold must lie between 0 and 1.

<P>Changing <B>Threshold gradient</B> from its default value of 0
causes a gradient to be apply to the previous threshold. Thus setting
a positive value here causes the primary threshold to be reduced at
the bottom of the brain, giving a larger brain estimate there, and a
smaller estimate of the brain towards the top of the image. This value
must lie between -1 and 1. It is even less likely that you will need
to change this threshold than the previous one.

<A NAME="bet"></A><HR><H2>bet COMMAND-LINE PROGRAM</H2>

<p>Type <b>bet</b> to get usage.
  
<A NAME="betfunc"></A><HR><H2>betfunc COMMAND-LINE SCRIPT</H2>

<p>Type <b>betfunc</b> to get usage; the input and output filenames
must be the filename roots (i.e. without the <b>.img</b> or
<b>.hdr</b>). This script uses <b>bet</b> to determine a brain mask on
the basis of the first volume in a 4D data set, and applies this to
the whole data set. This is principally intended for use on FMRI data,
for example to remove eyeballs. Because it is normally important (in
this application) that masking be liberal (ie that there be little
risk of cutting out valid brain voxels) the -f threshold is reduced to
0.3, and also the brain mask is "dilated" slightly before being used.

<p>Note that if you just use <b>bet</b> on 4D data, this will work;
the brain mask is derived from the first time point, and then applied
to all time points.

<A NAME="betpremask"></A><HR><H2>betpremask COMMAND-LINE SCRIPT</H2>

<p>Type <b>betpremask</b> to get usage; the input and output filenames
must be the filename roots (i.e. without the <b>.img</b> or
<b>.hdr</b>). This script uses <b>flirt</b> to register the input
image to a standard space whole-head image; the resulting transform is
then inverted and a standard-space brain mask is transformed into the
space of the input image, and then applied to this to create the
output.

<p><b>betpremask</b> can be useful if BET cannot be made to work
well.


<p><HR><FONT SIZE=1>Copyright &copy; 2000, University of
Oxford. Written by <A
HREF="http://www.fmrib.ox.ac.uk/~steve/index.html">S. Smith</A>.</FONT>

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