<usrguide name="FLIRT - FMRIB's Linear Image Registration Tool"
          rootdir="../"
          author="Mark Jenkinson"
	  affiliation="FMRIB Image Analysis Group"
	  year="1999-2000">

<data id="name"><link url="flirt/index.html">FLIRT</link></data>
<data id="description">FMRIB's Linear Image Registration Tool -
automatic accurate robust linear (affine) inter- and intra-modal
registration</data>
<data id="hasgui"><image src="images/tick.gif" alt="Y"></image></data>
<data id="hascli"><image src="images/tick.gif" alt="Y"></image></data>
<data id="version">1.1</data>

<section title="Introduction">
<p>
FLIRT is a fully automated robust and accurate tool for linear
(affine) inter- and inter-modal brain image registration.
</p>

<p>
For more detail on FLIRT and a journal reference, see the <link
url="http://www.fmrib.ox.ac.uk/analysis/research/flirt/">FLIRT web
page</link>. If you use FLIRT in your research, please quote the
journal reference listed there.
</p>
</section>

<section title="How it works">
<p>
<image src="xfmhelp.gif" align="CENTER"/>
</p>

<p>
In single-level registration, the reslice image is registered to the standard, and the resulting transform applied to the secondary
image(s). Thus the transformed reslice and secondary image(s) are in alignment with the standard image. 
</p>

<p>
In two-level registration, the low-res image (e.g. functional EPI image) is registered to the hi-res image (e.g. structural image) and
the hi-res is registered to the standard. The two resulting transforms are combined into one, and this is then applied to the low-res
and the secondary image(s). Thus the transformed hi-res, low-res and secondary image(s) are all in alignment with the standard
image. 
</p>
</section>

<section title="Suggested Usage">

<subsection title="Reslice Image/Group -&gt; Standard Image"> 
<p>
<itemize>
<item>To register an image to a standard template, put the name of
    template image (as found from the Page Manager) in the <guilabel>Standard
    Image</guilabel> box and the other in the <guilabel>Reslice Image/Group</guilabel> box.</item>
<item>To register two images to each other (where neither is the standard),
    put the higher resolution image in the <guilabel>Standard Image</guilabel> box and the
    other in the <guilabel>Reslice Image/Group</guilabel> box.</item>
<item>To do a number of different registrations (like you would in a
    script) to a single standard image, first make a group of all the
    images to be registered and then enter the Group page in the
    <guilabel>Reslice Image/Group</guilabel> box and the template image in the <guilabel>Standard Image</guilabel> box.</item>
</itemize>
</p>

</subsection>

<subsection title="Low Res Image/Group -&gt; High Res Image/Group -&gt; Standard Image"> 
<p>
<itemize>
<item>To register both a functional image and its corresponding structural to the standard image, put the template image in the
    <guilabel>Standard Image</guilabel> box, the structural image in the <guilabel>High Res Image/Group</guilabel> box and a single image from the functional series in
    the <guilabel>Low Res Image/Group</guilabel> box. In addition, statistical images such as Z-scores can be entered in as <guilabel>Secondary Images</guilabel> which
    will also be registered to the standard image, allowing them to be rendered on the structural image in the coordinate system of
    the standard image.</item>
<item>To do a number of registrations for different functional experiments (like you would in a script) requires that two groups of
    images be made. The first group should contain all the structural images and the second group should be a group of single
    functional images, one corresponding to each structural image. Note that the ordering of the images in these groups is critical
    - the functional example images must be in the same order as the corresponding structural images. Once the groups are made,
    enter the Group page of the structurals in the <guilabel>High Res Image/Group</guilabel> box and the Group page of the functionals in the <guilabel>Low
    Res Image/Group</guilabel> box. Any statistical images can be entered in as a <guilabel>Secondary Group</guilabel> but these must also be in the
    corresponding order. </item>
</itemize>
</p>

</subsection>
</section>

<section title="General Advice">
<itemize>

<item>DO use the default settings (especially in advanced options) as they have been carefully chosen.</item> 
<item>DO use it for registering to the MNI152 average as this is what it is designed to do well.</item> 
<item>DO use the Group facility for running the registration on a collection of images (this should avoid the need for scripting). </item>

</itemize>
</section>

<section title="Template Images">

<p>MNI152 template images (whole head, extracted brain, brain
mask and skull) are included in fsl/data/standard, courtesy of the
<link url="http://www.mni.mcgill.ca/">MNI</link>.</p>

</section>

</usrguide>
