I would start by checking whether the initial FLIRT-based registration
has worked successfully - this is likely the cause of the problem -
and if so then tweak the registrations.
Cheers.
On 13 Feb 2009, at 03:51, Michael Scheel wrote:
> Dear fsl experts,
>
> i am using FIRST to segment the Hippocampus in a T1 dataset of 84
> different volumes. In some cases FIRST does an excellent job and in
> some cases it's just really awfully wrong - the position of the
> hippocampus is getting estimated deep in white matter. I was
> wondering how I could improve the results, e.g. Noise reduction of
> the original T1 (maybe with SUSAN) or correct for intensity
> inhomogeneity how it is done in FAST.
> Or are these steps included in the FIRST script?
>
> Thanks a lot, Michael
>
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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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