Hi,
On 6 Jul 2007, at 02:43, Dianne Patterson wrote:
> Dear group,
>
> I am running fast on an inversion recovery spgr voxels 1x1x1.4.
> I am having trouble getting fast to distinguish the basal ganglia.
> Our eventual goals are:
> A) to get a good estimation of total gm and wm and a brain volume
> B) to use the white matter image as a mask to help segment out WM
> hyperintensities from a flair image.
>
> I have run bet and manually edited the bet result to remove eyeball
> and check for other problems.
> I have used the bias corrected image (this seems to help...but not
> enough)
> I have tried segmenting into 4 classes instead of three (this did
> not seem to help)
>
> It has been suggested to me that I should remove the central core
> of the brain and segment it separately...and I am getting close to
> trying that option...
> Because we will be processing elderly brains, my colleagues would
> prefer that I avoid bayesian priors and posteriors.
>
> 1) Could anyone suggest alternative ways to run fast that might
> help...
> 2) Would anyone care to comment on the brain coring method (are
> there obvious problems with it, or does it sound like a good idea)
If it works, then sure - go ahead. An alternative might be to do one
segmentation with the -A option and another without, and just take
the central results from the first and the cortical results from the
second. However, the best approach should be to use FIRST in
conjunction with FAST. FIRST (FMRIB's Integrated Registration and
Segmentation Tool) explicitly models the subcortical structures from
a T1, so may be useful here. FIRST will be available in the next
release of FSL, in a few weeks hopefully.
Cheers, Steve.
>
> Other thoughts?
>
> Thankyou for your time,
>
> Dianne
>
> --
> Dianne Patterson, Ph.D.
> [log in to unmask]
> ERP Lab
> University of Arizona
> 621-3256 (Office)
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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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