I wrote this script to automate and simplify BET tool (FSL) without writing any command line. User only needs to specify data directory and to select options at the beginning. To download this script please click on the following link

http://www.easyneuroimaging.com/2011/12/...

[color=blue]BET[/color] (Brain Extraction Tool) deletes non-brain tissue from an image of the whole head. It can also estimate the inner and outer skull surfaces, and outer scalp surface, if you have good quality T1 and T2 input images.