| FSL User Guide - Overview of the FLIRT project
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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.
For each of the programs described here, a full list of available options
can be obtained by running the command with no options.
FLIRT
flirt is the main program that performs affine registration. It takes
an input (-in) and a reference
(-ref) volume, and then calculates the affine
transformation that registers the input to the reference. The
transformation can be saved as a 4x4 affine matrix
(-omat) or as a MEDx transform
(-omedx).
In addition, FLIRT can also be used to apply a saved transformation to
a volume (-applyxfm and -out). For
this usage the reference volume must still be specified as this sets
the voxel and image dimensions of the resulting volume.
CONVERT_XFM
convert_xfm is a utility that is used to convert between different
transformation file formats. It can read and write ascii 4x4 matrices
and MEDx transforms as well as reading MINC transform files. In
addition, it can be used to concatenate two transforms (using
-concat with the second transform) or to find the
inverse transformation (using -inverse).
As MEDx transformations require voxel dimensions, the input and
reference volume corresponding to the transformation must be specified
when using this command. However, if only ascii files are used, the
-matonly option can be used, in which case no volumes
need to be specified.
RMSDIFF
rmsdiff 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.
AVSCALE
avscale 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).
Mark Jenkinson
Copyright © 2000, University of Oxford