thanks
-----Original Message-----
From: Stephen Smith [mailto:[log in to unmask]]
Sent: Tuesday, January 08, 2002 11:33 AM
To: [log in to unmask]
Subject: Re: [FSL] brain extraction
Hi - thanks for sending the example images. Yes - there's no problem with
these - you need to change the "Fractional intensity threshold" under
Advanced options in the BET GUI (or if using BET on the command line or
within the SIENA scripts use the -f option inside the scripts)
For proton density you need to select 0.3
( command line: bet <in> <out> -f 0.3 )
For T2 (a quite dark, noisy image) you need to select 0.1
Hopefully then everything will be fine!
Thanks, Steve.
Stephen M. Smith
Head of Image Analysis, FMRIB
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
On Tue, 8 Jan 2002, Marenco, Stefano (NIMH) wrote:
> When I read the advanced options I could not make much sense of them. I
have
> a acquired images with an inversion recovery pulse t2 and proton density
> weighted. When I try to extract brain I get a much too small contour of
the
> brain, for example at the top of the head only the longitudinal fissure
and
> a little bit of tissue around it was preserved. The background skull
tissue
> has very low signal and the images are fairly noisy since they are 1.5 mm
> thick. I can send you both sets in a tar file if necessary, but maybe you
> could suggest what advanced options to use first.
>
> Stefano
>
> -----Original Message-----
> From: Stephen Smith [mailto:[log in to unmask]]
> Sent: Saturday, January 05, 2002 1:28 PM
> To: [log in to unmask]
> Subject: Re: [FSL] brain extraction
>
> hi - sorry for the delay in answering. What kind of problems are you
> having with these images? I assume you've tried playing with the "advanced
> options" in the GUI?
>
> ttfn ;-)
>
> Stephen M. Smith
> Head of Image Analysis, FMRIB
>
> 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
>
> On Wed, 2 Jan 2002, Marenco, Stefano (NIMH) wrote:
>
> > I am having trouble extracting the brain from proton density and t2
> weighted
> > images. Any suggestions?
> >
> > Stefano Marenco, M.D.
> > Senior Staff Fellow, NIMH, CBDB
> > Bldg 10 room 4S235
> > 9000 Rockville PIke
> > Bethesda, MD 20892
> > email: [log in to unmask]
> > tel: (301) 435-8964
> > fax: (301) 4807795
> >
>
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