FSL User Guide - Overview of the FLIRT project


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