<usrguide name="Overview of the FLIRT project" section="l" rootdir="../" author="Mark Jenkinson" 
year="2000">

<section title="Introduction">
This document gives a brief description of the various command line
programs available in the FLIRT component of FSL.  A description of
the GUI interface is contained in another document.

<p>
For each of the programs described here, a full list of available options
can be obtained by running the command with no options.
</p>
</section>


<section title="FLIRT">
<type>flirt</type> is the main program that performs affine registration.  It takes
an input (<attrib>-in</attrib>) and a reference
(<attrib>-ref</attrib>) volume, and then calculates the affine
transformation that registers the input to the reference.  The
transformation can be saved as a 4x4 affine matrix
(<attrib>-omat</attrib>).

<p>
In addition, FLIRT can also be used to apply a saved transformation to
a volume (<attrib>-applyxfm</attrib> and <attrib>-out</attrib>).  For
this usage the reference volume must still be specified as this sets
the voxel and image dimensions of the resulting volume.
</p>
</section>


<section title="CONVERT_XFM">
<type>convert_xfm</type> is a utility that is used to convert between different
transformation file formats.  It can read and write ascii 4x4 matrices.  In
addition, it can be used to concatenate two transforms (using
<attrib>-concat</attrib> with the second transform) or to find the
inverse transformation (using <attrib>-inverse</attrib>).


</section>

<section title="RMSDIFF">
<type>rmsdiff</type> is a utility that calculates the Root Mean Square deviation
(in millimetres) between two transformations.  That is, it compares
two transformations (normally two possible registrations of the same
volume pair) to see how much they differ.  This is useful to compare
alternative registrations.
</section>

<section title="AVSCALE">
<type>avscale</type> is a utility that displays the decomposed elements of an
affine matrix.  It displays the rotation/translation matrix, the
individual axis scalings, the individual skews, the average scaling,
and the forward and backward halfway transformations.  In order to set
the centre of rotation it requires the input volume (also called the
reslice volume).
</section>


</usrguide>
