Hi - we don't have a very sophisticated solution to this issue, but here
is what we do have: if you register to standard space using FLIRT, invert
the transform using convert_xfm, and then apply this to the standard-space
mask fsl/etc/standard/avg152T1_strucseg.hdr you can get different masks
for these different regions. To the extent that a given subject transforms
well linearly into standard space these masks may prove useful.
Cheers.
On Wed, 12 Nov 2003, Johannes Klein wrote:
> Hello everyone,
> I'm trying to segment the cerebral cortex out of T1-weighted MRIs. Does
> anyone have recommendations how to avoid including subcortical structures,
> and possibly also to get rid of the cerebellum in the process without
> manually removing these objects? I've tried using a combination of
> erode/dilate-operations with component analysis on the result of FAST, which
> gives reasonable, yet imperfect results. Maybe someone else has tackled this
> problem already?
> Thanks for your help
> Johannes
>
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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