Hi,
On 12 Feb 2008, at 22:36, Aaron Trachtenberg wrote:
> Hi,
> I am a student learning to use FSL with a dataset that has a lot of
> neck in the images. Does the BET within FEAT using the robust (-R)
> type of brain extraction or should I run BET -R on the fMRI images
> before putting them through FEAT?
Are you saying that the FMRI data has lots of neck? Unlikely.....but
possible. Anyway, if BET run by FEAT on the FMRI doesn't work well,
you could try just turning it off. It's not generally too important to
run BET on the FMRI.
But it is important to run it on the structural data, which you need
to do before running FEAT.
>
> Also, just to be sure, am I supposed to run BET on the structural
> image used in the registration before running FEAT, in other words,
> does the BET within FEAT only applies to the functional images and
> not the images used in the registration part??
That's right.
Cheers.
>
> Thanks a lot
> Aaron Trachtenberg
>
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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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