Hi - no, those areas are part of the brain. I think you are
mis-identifying them because in your image the eyeballs are dark.
BET has not changed much in the last couple of years, so the version you
are running is probably fine.
Thanks, Steve.
On Thu, 10 Jul 2003, QingYan Guan wrote:
> Hi,
> Thanks for quick response.
> Yes, I used only bet.
> Do you mean you used bet with default f and g, and you got very nice image?
>
> I am not sure if I am right. But in the first 2 and 3 slice after my bet
> extraction, there are two big dot above the brain, isn't it? I think that is
> eyeball.
>
> Do you think a fsl old package (Medx builtin) would be the reason for
> getting bad images? I used old one.
>
> Thanks, Qingyan
>
> ----- Original Message -----
> From: "Stephen Smith" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Thursday, July 10, 2003 1:12 PM
> Subject: Re: [FSL] bet on fmri image
>
>
> > Hi - are you using bet or betfunc to brain-extract this data? If you just
> > run the default bet then you get a very nice brain-extraction, given the
> > low resolution of FMRI data.
> >
> > I'm not sure what you mean by getting rid of eyeballs - eyeballs are
> > almost not visible in this particular image, and it certainly doesn't look
> > like bet includes where they would be?
> >
> > Thanks, Steve.
> >
> >
> > On Thu, 10 Jul 2003, QingYan Guan wrote:
> >
> > > Hello,
> > >
> > > I have one group of fmri dataset. I want to extract the brain for each
> 3D
> > > volume seperately.
> > >
> > > But I couldn't get good image. I can't get rid of eyeballs. I have tried
> > > different f g value, but it seems not working very well.
> > > Is it because of fmri low resolution image?
> > >
> > > Any suggestion? Thanks a lot!
> > >
> > > If you could look at the dataset below, that will be really greatful
> > > help.Thanks.
> > > http://staff.washington.edu/qguan/fmri_bet
> > >
> > > Best regards,
> > >
> > > QingYan
> > >
> >
> > Stephen M. Smith MA DPhil CEng MIEE
> > 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
> >
>
Stephen M. Smith MA DPhil CEng MIEE
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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