Hi, this is covered a little in the manual and the FLIRT and FEAT
lectures in the FSL course lecture downloads; the main thing to look
at carefully is whether the registration is working well, normally
you need to reduce the DOF and possibly include an extra "initial
structural" image in the registration chain.
Cheers.
On 10 Jul 2007, at 19:25, [log in to unmask] wrote:
> Thank you, Steve.
>
> Is it a problem for FEAT if there is a limited FoV in the EPI data?
> Anything you can think about I should check or need to consider in
> this regard?
>
> Thanks a lot!
>
> Sandy
>
> Steve Smith <[log in to unmask]> wrote: Hi,
>
> On 9 Jul 2007, at 17:20, [log in to unmask] wrote:
>
> > Hi,
> >
> > I am am running FSL 3.3 and have the following two questions, which
> > might be silly, but nevertheless I can't answer for myself.
> >
> > 1. When defining the input 4D data set during a firdt level
> > analysis, I get the following warning:
> > "Warning - have auto-set BET preprocessing option and/or
> > registration DoF on the basis of image fields; check settings"
> >
> > Any idea why this is coming up. Is this warning important?
>
> This is probably because you have limited field-of-view in your data,
> probably in the Z direction.
>
> > In the design setup, I have "BET brain extraction" selected, and
> > "main structural image" for registration is skull-stripped.
> >
> > 2. For a different analysis I want to display the 1stlevel results
> > on the high-res anatomical of the individual subject without
> > distorting the high-res structural in any way. Under "Registration"
> > I have selected only "Standard Space" and have supplied the high-
> > res skull-stripped structural MRI of that subject. Other options
> > are linear normal search. I obviously want to do rigid-body
> > registration only, so I select DOF = 6. But for some reason FSL
> > seems tyo default back onto DOF = 7. What is the difference here?
> > Would you recommend 6 or 7 DOFs?
>
> It probably doesn't matter. You could try both, but either should be
> ok if your EPI is well calibrated in the same way as the structural.
>
> Cheers.
>
>
>
> >
> > Thanks a lot!
> >
> > Sandy
> >
> >
> > The fish are biting.
> > Get more visitors on your site using Yahoo! Search Marketing.
>
>
> ----------------------------------------------------------------------
> --
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR 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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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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