FLIRT - FMRIB's Linear Image Registration Tool
FLIRT v5.5 - User Guide
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INTRODUCTION
FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated
robust and accurate tool for linear (affine) intra- and inter-modal
brain image registration.
For more detail on FLIRT and an updated journal reference, see the FLIRT research
web page. If you use FLIRT in your research, please quote the
journal reference listed there.
The different FLIRT programs are:
If you want to register FMRI data with only a few slices, then see here.
GENERAL ADVICE
- Use the image with the best quality (tissue contrast and resolution)
as the Reference image, otherwise poor registrations may occur (the inverse
transformation can be found afterwards using the InvertXFM gui or the convert_xfm command-line utility).
- Do use the default settings (especially in the GUI advanced
options) as they have been carefully chosen.
- Do use it for registering to the MNI standard brains as it has been
extensively tested with these images.
- For images showing pathology, consider using binary cost function weighting
images - a zero for areas of a pathological nature and one elsewhere (do not put zero outside the brain).
- Consider using the Group facility (GUI only)
for running the registration on a collection of images (this is also easily
achieved with the command-line version by scripting).
TEMPLATE IMAGES
Both linearly and non-linearly generated MNI152 template images
(whole head, extracted brain, brain mask and skull) are included in
fsl/data/standard, courtesy of the MNI.
NON-LINEAR REGISTRATION
Also see the FSL non-linear registration tool, FNIRT. Note that this requires an initial affine registration to be performed first using FLIRT.
Copyright © 2001-2008, University of
Oxford. Written by Mark Jenkinson.