BET2 - Brain Extraction Tool - User Guide BET Version 2.0

INTRODUCTION

BET (Brain Extraction Tool) deletes non-brain tissue from an image of the whole head. It can also estimate the external skull surface.

BET2 is a new version of the original bet C program, with the additional functionality of also being able to estimate inner and outer skull surfaces, and outer scalp surface, if you have good quality T1 and T2 input images. BET2 comprises two main programs:

• bet2 - a direct recoding of bet into c++, with close to identical results
• betsurf - using a registered T1 and T2 image pair, estimates inner and outer skull surfaces and outer scalp surface

Note that BET v2.0 should be considered a "beta release" as it has not yet been very widely tested. There is not yet a GUI for bet2.

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

bet2

bet2 has virtually the same functionality as the original bet command-line program. You can use the same command-line syntax as before, with the main addition being the -e option for outputting a "mesh" version of the estimated brain mask.

betsurf

betsurf is the program that produces the three additional surfaces (inner & outer skull, outer scalp). It can output these surfaces as filled-in binary mask images, surface-only binary mask images and Geomview mesh format files.

betsurf requires ideally good resolution T1- and T2-weighted input images. It can work only from just a T1 image, but the results will generally not be as good. The images should ideally be better than 2x2x2mm - the smaller the voxel size the better. betsurf requires that bet2 has already been run on the T1 image, with the -e mesh output option for the brain surface. It also requires that the T2 image already be aligned (e.g., using flirt) to the T1. Finally, it requires that you supply a transformation from the T1 to standard space (e.g., generated by flirt) as it uses standard-space masks in order to constraint some of the mesh fitting.

As an example of how to use bet2 and betsurf together, see the betall script (in $FSLDIR/bin). This:

• Registers the T2 to the T1 image.
• Registers the T1 image to standard space (not to transform the image but just to get the transform matrix itself).
• Runs bet2 to get the initial brain extraction from the T1 image.
• Runs betsurf to get the other head surfaces.