Hi - yes, though BET is insensitive to orientation (unless you're using
the -g flag) the registration in SIENA doesn't do a full angular search if
you are using registration to standard space - so you might want to change
the FLIRT option to cinlude full search.
Cheers, Steve.
On Fri, 22 Oct 2004, Valerie Anderson wrote:
> I have recently run SIENA on a set of coronal images, but the results from
> the BET segmentation were dissapointing and included tissue between and
> below the temporal lobes.
>
> Although I had read that the programs involved in SIENA do not recognize
> which format the input images are in, I wondered whether reorienting the
> images to axial format would help, so I reoriented them.
>
> Although the BET regions I obtained from the axially oriented images were
> similar to those obtained when running SIENA on the coronal images, the
> results of the registration and quantification of change were different
> (better in the case of the registration). How can this be explained?
>
> Thanks,
> Valerie Anderson
>
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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