Hi there -
I'm not sure whether this is the same problem - However, if it is,
it is because the default sphere initialisation in the released
version of bet runs outside the brain, so, you crop the image to
make sure the initialisation is ok.
However there is now a new version of bet which lets you specify you're
initialisation sphere, so you no longer have to bother with cropping etc.
For Linux:
Download all the Linux binaries in:
http://www.fmrib.ox.ac.uk/~steve/ftp/bet_linux/
and put them in
$FSLDIR/bin/
and then use -c for centre and -r for radius of the initial sphere. Make
sure it is all within the brain.
Hope this helps
Cheers
Tim
On Wed, 28 Aug 2002, E.J.P. Vlieger wrote:
> What worked in my situation was to crop the image such that it only
> included brain. Use avwroi for that.
>
> Erik-Jan
>
> ----- Original Message -----
> From: Adolf Pfefferbaum <[log in to unmask]>
> Date: Wednesday, August 28, 2002 10:29 pm
> Subject: Re: [FSL] BET
>
> > I am trying to use bet on T1 SPGR images. I continue to have high
> > signalintensity tissue (probably fat) remaining anterior to the
> > pons and along
> > the optic nerves and eyeballs. I have tried some different -f and
> > -g
> > values with little success. Any suggestions?
> >
> > Thanks,
> >
> > Dolf
> >
> > _______________________
> > Adolf Pfefferbaum,MD
> > Neuroscience Program
> > SRI International
> > 650-859-2927 phone
> > 650-859-2743 FAX
> >
>
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Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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