You shouldn't normally need to BET the diffdata. It largely depends upon how the mask is being generated - it should be possible to determine this from the log file. In general, with FSL 5.0.06, you need to BET any 'structural' images and this includes any image you enter into the --regfrom command.
Michael
On 15 Jan 2014, at 12:41, R. Duke <[log in to unmask]> wrote:
> Hi,
>
> When running oxford_asl my output mask.nii.gz file does not isolate the brain (it includes the entire image). Should I BET the diffdata image before I run oxford_asl? I am currently running 5.0.6.
>
> Cheers,
>
> R
>
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