Thanks Mark!
jack
>Hi Jack,
>
>Sorry I haven't answered this before, I've been out of the lab quite a
>lot.
>
>As for motion correction:
>1 - we've only written motion correction to deal with a minimum of 6 dof
> properly for 3D data, but it should only use 3 dof for 2D data.
>2 - one slice will be picked as a reference and all other slices aligned
> with the slice in your case (which slice can be selected using
>-refvol).
> This isn't really what you want. I think you'd be better off
>scripting up
> flirt calls rather than trying to do this with mcflirt, but this
>problem is
> still very difficult and I don't know that you'll have a lot of
>success.
>
>For modelling, the second option does make the most sense to me.
>
>All the best,
> Mark
>
>
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