Hi - you probably want to apply the same mask for all volumes, and be
doing that after motion correction (if you're doing that), in which case
you probably want betfunc which is a simple script wrapper for applying
BET to FMRI data. This uses the first time point as the input to BET.
If you do want to run BET separately on each volume (which is unlikely)
then use avwsplit, bet and avwmerge.
Cheers, Steve.
On Wed, 22 Sep 2004, Wolf Zinke wrote:
> Hi,
>
> When using bet on a 4D data set I get a 3D brain mask.
> - What Volume is used to calculate the mask or is it based on an average
> image?
> - Is there a way to tell bet to calculate a mask for each volume
> sepparately or do I have to split a 4D dataset, run bet on each single 3D
> volume and merge the dataset later again?
>
> Thanks,
>
> wolf
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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