FSL User Guide - FLIRT - FMRIB's Linear Image Registration Tool


INTRODUCTION

FLIRT is a fully automated robust and accurate tool for linear (affine) inter- and inter-modal brain image registration.

For more detail on FLIRT and a journal reference, see the FLIRT web page. If you use FLIRT in your research, please quote the journal reference listed there.


HOW IT WORKS


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.

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.


SUGGESTED USAGE

Reslice Image/Group -> Standard Image


Low Res Image/Group -> High Res Image/Group -> Standard Image



GENERAL ADVICE


TEMPLATE IMAGES

Talairached template images (whole head, extracted brain, brain mask and skull) are included in fsl/etc/standard, courtesy of the MNI.


Mark Jenkinson
FMRIB Image Analysis Group

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