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No - the standard usage is to use the whole head image. However, if you have trouble with the registration step it can sometimes help to use BET. Try it without first and see if that works. All the best, Mark On 10 Jan 2011, at 08:52, Mailinglisten Lifeandbrain wrote: > Dear FSL-Team, > > is it recommended to run BET before FIRST? > > Thanks! > Jan