Hi - yes, if you just use -B then the skull is created at the
beginning and the mask at the end, and it agrees with the brain
extracted. This is the recommended way of doing things.
Cheers.
On 31 Aug 2007, at 12:21, Brandon Whitcher wrote:
> I have been playing around with bet in FSL v4.0 and I have a
> question about
> the order in which operations are performed.
>
> It appears that skull (-s) and binary (-m) masking occurs before
> some of the
> more elaborate processing options in BET. For example, I have a BET
> execution with -B (for neck and bias field correction) that
> produces a brain
> extraction that looks nothing like the binary mask. In the script,
> the
> steps for "variation=7" occur after the production of a binary
> mask. Is
> this correct? I can understand the skull estimation needs to be
> first. I
> thought the binary mask would be simply a 0/1 version of my final
> brain
> extraction, but this doesn't appear to be the case.
>
> thanks,
>
> Brandon
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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