Hi - yes, that does sound sensible. These aren't things we've investigated
in great detail. I guess if you have a lot of head motion then you might
need affine as well for within-direction averaging, if there was
interaction between eddies and head motion. Another finesse is that your
approach will end up interpolating each image twice, and with a bit more
bookkeeping you should be able to avoid that - not sure if it's worth the
effort though. Any thoughts on that, MJ or Tim?
Cheers.
On Thu, 8 Jul 2004, Russ Poldrack wrote:
> >
> > Strange - this must be a platform-dependent bug, as it works fine on my
> > mactop, and gives good results too. What platform are you using?
> >
> > However, anyway: the attached script eddy_correct (which will be part
> > of
> > FDT, the diffusion toolkit, when it's released later this summer) uses
> > FLIRT instead of mcflirt to realign diffusion data, the point being
> > that
> > when you have eddy currents you need affine alignment not rigid body,
> > which is more of an issue with diff data...you might want to try that
> > instead, though on this data it seems to give similar results.
> >
> > Cheers.
> >
> Steve,
> thanks for the script. I'm running on linux (suse 9.0). What I was
> doing was first using mcflirt to realign the individual runs separately
> for each diffusion direction (we generally collect 4-5 runs), taking
> the mean for each direction, then using flirt with 12 dof and mutual
> information to align across the different diffusion directions. Does
> that sound reasonable? The data that I sent were all for a single
> direction, which is presumably why the results of flirt and mcflirt are
> similar.
>
> cheers
> russ
> ---
> Russell A. Poldrack, Ph.D.
> Assistant Professor of Psychology, UCLA
> Franz Hall, Box 951563
> Los Angeles, CA 90095-1563
> email: [log in to unmask]
> phone: 310.794.1224
> fax: 310.206.5895
> web: http://www.poldracklab.org/
>
Stephen M. Smith DPhil
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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