It does per default - because the skull etsimate is used for scaling (as, for example, scanner calibration may change slightly over time).
Cheers-
Andreas
________________________________
Von: FSL - FMRIB's Software Library im Auftrag von John Ollinger
Gesendet: Do 29.11.2007 18:54
An: [log in to unmask]
Betreff: Re: [FSL] SIENA
Donald,
I don't see how the type of brain stripping could matter to sienna.
John
On Nov 29, 2007 11:29 AM, MCLAREN, Donald <[log in to unmask] > wrote:
But can we use these images with SIENA or does SIENA require that BET
is used as an intermediary stage?
On Nov 29, 2007 11:28 AM, MCLAREN, Donald <[log in to unmask]> wrote:
> But can we use these images with SIENA or does SIENA require that BET
> is used as an intermediary stage?
>
>
> On Nov 29, 2007 11:05 AM, John Ollinger <[log in to unmask]> wrote:
> > Donald,
> >
> > I also have found bet to be ineffective in some cases. There is an
> > "improved" version in the latest version of fsl, but I am not sure it is
> > that much better. I have heard that people have been getting much better
> > results with AFNIs 3dskullstrip program. You might try that.
> >
> > John
> >
> >
> >
> > On Nov 29, 2007 10:32 AM, MCLAREN, Donald < [log in to unmask] <mailto:[log in to unmask]> > wrote:
> > > Dear All,
> > >
> > > I'd like to use SIENA; however, BET seems to consistently fail on my
> > > subjects. A couple of quick questions:
> > > (1) I have images that have been deskulled (and could easily get
> > > images of the skulls);
> > > (2) I have a customized deskulled template (and could create a skulled
> > > template).
> > >
> > > Is there anyway to use SIENA with images that have been deskulled
> > > outside of the SIENA processing stream and to use a different
> > > template.
> > >
> > > Any thoughts would be appreciated.
> > >
> > > --
> > > Best Regards, Donald McLaren
> > > =====================
> > > D.G. McLaren
> > > University of Wisconsin - Madison
> > > Neuroscience Training Program
> > > Tel: (773) 406 2464
> > > =====================
> > > This e-mail contains CONFIDENTIAL INFORMATION which may contain
> > > PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED
> > > and which is intended only for the use of the individual or entity
> > > named above. If the reader of the e-mail is not the intended recipient
> > > or the employee or agent responsible for delivering it to the intended
> > > recipient, you are hereby notified that you are in possession of
> > > confidential and privileged information. Any unauthorized use,
> > > disclosure, copying or the taking of any action in reliance on the
> > > contents of this information is strictly prohibited and may be
> > > unlawful. If you have received this e-mail unintentionally, please
> > > immediately notify the sender via telephone at (773) 406 2464 or
> > > email.
> > >
> >
> >
> >
> > --
> > John Ollinger
> > University of Wisconsin
> > Waisman Center, T233
> > 1500 Highland Ave
> > Madison, WI 53711
> > http://brainimaging.waisman.wisc.edu/~jjo/
>
>
>
> --
>
> Best Regards, Donald McLaren
> =====================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Tel: (773) 406 2464
> =====================
> This e-mail contains CONFIDENTIAL INFORMATION which may contain
> PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED
> and which is intended only for the use of the individual or entity
> named above. If the reader of the e-mail is not the intended recipient
> or the employee or agent responsible for delivering it to the intended
> recipient, you are hereby notified that you are in possession of
> confidential and privileged information. Any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the
> contents of this information is strictly prohibited and may be
> unlawful. If you have received this e-mail unintentionally, please
> immediately notify the sender via telephone at (773) 406 2464 or
> email.
>
--
Best Regards, Donald McLaren
=====================
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Tel: (773) 406 2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain
PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED
and which is intended only for the use of the individual or entity
named above. If the reader of the e-mail is not the intended recipient
or the employee or agent responsible for delivering it to the intended
recipient, you are hereby notified that you are in possession of
confidential and privileged information. Any unauthorized use,
disclosure, copying or the taking of any action in reliance on the
contents of this information is strictly prohibited and may be
unlawful. If you have received this e-mail unintentionally, please
immediately notify the sender via telephone at (773) 406 2464 or
email.
--
John Ollinger
University of Wisconsin
Waisman Center, T233
1500 Highland Ave
Madison, WI 53711
http://brainimaging.waisman.wisc.edu/~jjo/
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