FLIRT: FMRIB's Linear Image Registration Tool - User Guide FLIRT Version 5.0

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:

• Flirt - FLIRT GUI + InvertXFM, ApplyXFM, ConcatXFM
  
• flirt - command-line FLIRT program
  
• misc flirt utilities - associated command-line programs
  

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 Talairaching with 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

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