Hi,
All 3 of your emails seem to be asking the same question.....so I'll
just reply to the most recent:
I'm surprised that you're seeing a difference between the old BET and
BET2, as they are virtually identical algorithms that get run by
default. I suspect that you are more likely talking about the complete
masking process carried out by FEAT rather than just the effect of the
brain extraction? In any case it's not generally important to get the
FMRI masking/brain-extraction very accurate - it can just be liberal
(i.e. over-inclusive). You can achieve that by changing things like
the threshold value in the FEAT GUI.
Cheers.
On 23 Jul 2008, at 19:03, Diederick wrote:
> Dear all,
>
> Bet2 in FSL4 does not do a good job at skull stripping our EPI
> sequences
> (bet –F –f 0.6 –g 0.5). We have tried playing around with f and g,
> but no
> satisfactory results. We either see remaining skull or stripping which
> includes part of the brain. The old bet version in FSL3.3 does a
> great job,
> however (this is what we are using for now, as we appear to be
> unable to use
> bet2 on 4D data without the –F option). The new version does a
> really good
> job at single volumes in our 4D data. We would obviously prefer
> doing are
> full analysis in FSL4. How should we go about this? The only option
> I see
> now is splitting the 4D data in individual volumes and merging them
> again
> after bet2. Help would be greatly appreciated.
>
> Cheers
>
> Diederick
>
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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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