Hi Darren,
In theory BET can give good results on all of these image types
separately. You can't feed multiple images into BET, though you could
combine the BET masks from the separate runs with various logic, assuming
that they have all be aligned. FAST however can take multiple inputs for
the tissue-type segmentation.
Your question about slight variations in BET output across the modalities
is a good worry, and something to keep in mind, although in my experience
it has not proved a cause of misalignment. As you say, it may be safer to
run FLIRT before running BET.
FLIRT's default cost function is correlation-ratio, which IS a inter-model
cost function (like mutual information); in general it seems to behave a
little more nicely than MI.
Thanks, Steve.
On Sun, 16 Feb 2003, Darren Weber wrote:
> Dear Steve, Mark et al,
>
> can BET handle multiple contrast volumes, T1/T2/PD?
>
> Is there any way these volumes can be brain extracted and/or segmented at
> the same time (perhaps using mutual information techniques)?
>
> Lets assume an ideal situation where these anatomical volumes were the same
> dimensions and perfectly coregistered before using BET (assume no subject
> movement during scanning of all volumes & steady Bo fields etc). What are
> the chances that processing the volumes individually with BET (assuming it
> can handle all contrast images) could introduce variations in boundary
> intensity that could lead FLIRT to "misalign" the volumes?
>
> I assume that FLIRT can coregister T1/T2/PD volumes using a mutual
> information cost function. Would this be the best cost function for this
> process?
>
> Best regards, Darren
>
>
> --
> Darren Weber, PhD Student
> Cognitive Neuroscience, School of Psychology
> Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
> Ph: (61 8) 8201 3998, Fax: (61 8) 8201 3877
> http://brain.mhri.edu.au/~dlw/homepages/index.html
>
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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