Hi - you could try setting the "centre" with the -c option - if you load
the image into FSLView and click in the centre of the brain, take the (mm)
co-ordinates and put them into the -c option with bet. If this doesn't
work feel free to email us directly an example image and we can have a
play.
Cheers, Steve.
On Thu, 22 Jan 2004, Lee, Sang wrote:
> Dear, FSL users...
>
> I'm quite a newbie at FSL.
> I wanted to run BET on some of our 3D T1 images.
>
> In some images, the segmentation is wonderful, however in some cases, some
> of non-brain matter below the brain and eye-socket are not removed.
> I tried to raise the Fractional intensity threshold, but that removes brain
> matters as well.
> Also, CSF comes out to be larger than grey or white matter when I perform
> FAST on those ones that have problem.
>
> Is there something that i can do to improve the segmentation?
>
> Image sets that are having these problems have following scan parameters:
> Slice thickness = 1.5
> FOV =24
> TR = 9
> TE = 1.8
> FA = 10
>
> Image sets that are great with BET and FAST have following scan paramters:
> slice thickness = 1.2
> FOV = 25
> TR = 20
> TE = 6
> FA = 20
>
> Both are 3D-SPGR images.
> Can any of you tell me what factors might affect BET and FAST procedures and
> the solution for those problems?
>
> Thank you very much.
>
> Aaron****************************EMAIL
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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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