Hi - there are some hints at
http://www.fmrib.ox.ac.uk/fslfaq/#bet_animal
Also, as well as the -c and -r options, you may want to increase the
voxel dimensions to be say a factor of 10 larger than they actually
are (that may help, not sure) - and also, if the brains are long and
thin, it might help to reduce the voxel dimension in the long axis so
that BET thinks it's more spherical in real space - that can help.
Cheers, Steve.
On 28 Jun 2006, at 18:20, Henryk Faas wrote:
> Hi
> does anyone have experience using BET (in fsl) to extract mouse brains
> from MR images?
> BET does a good job in the central coronal slices of my 3D (isotropic)
> volume, presumably where the spere originates, but then does not
> do so
> well towards the front or back of the brain. It seems that that a
> higher
> fractional intensity threshold (0.9), it basically cuts along the
> shape
> of the sphere, at a lower (o.65), it takes too much of tissue
> outside the
> brain, but still cuts off the cerebellum.
> Thanks for your help!
> Henryk
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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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