Hi - no, FLIRT will have corrected for the different voxel sizes - if the
registration overlays look ok then any weird looking stuff in the
activation overlays can't be due to registration-related issues. It might
be worth you putting the full FEAT directory on a website so we can have a
look at the effects you are worried about.
Cheers, Steve.
On Wed, 19 May 2004, Jane Aspell wrote:
> Steve,
> some more points to add to the previous query...even though the
> registration page on the feat report looks ok my activations on highres
> overlay doesn't. i wondered if the problem might be a failure to match
> pixel sizes in the different images. for one subject both 24 slice
> functional EPI and 120 slice EPI ('initial sturctural') have pixdims
> 3,3,3 but for another subject the 120 slice is 4,4,3. i don't know why
> the latter is different for one of the subjects. could this difference
> between the 24 slice and 120 slice image for one of the subjects be
> causing a problem? and do i need to set some parameter (eg one of the
> advanced options) in flirt to allow for the fact that my 24 slice
> functional EPI (and 120 slice EPI) has slices at an oblique angle?
> thanks for your help
>
> Jane
>
>
>
> In message
> <[log in to unmask]> FSL
> - FMRIB's Software Library <[log in to unmask]> writes:
> > Hi - it's difficult to judge registration quality by looking at the
> > activation overlay - you should be clicking on the registration
> > evaluation image towards the bottom of the FEAT webpage report and
> > look at the detailed registration evaluation images - do they look ok?
> >
> >
> > Cheers, Steve.
> >
> >
> > On Mon, 17 May 2004, Jane Aspell wrote:
> >
> > > Hi
> > >
> > > I'm having some problems registering my functional data onto a highres
> > > image of an individual subject's brain. My functional data is in the
> > > form of 24 obliquely oriented slices mainly covering the occipital
> > > area (it's a vision study). The clusters of activation seem to 'flame
> > > out' from the brain in some areas, into 'space' by a few millimetres.
> > > This problem seems to be worse in occipital areas and not so bad in
> > > parietal areas. I have an idea that occipital areas are subject to
> > > more distortion than other areas - is this true? To register my
> > > functional to a highres with flirt i did a 7 parameter global rescale
> > > transformation from my 24 slice functional data to a 120 slice EPI
> > > (slices at the same angle as the functional) and another 7 param
> > > global rescale to my individual highres structural. is there anything
> > > you could advise i do to improve my registration?
> > >
> > > many thanks for your time,
> > >
> > > Jane Aspell
> > >
> >
> > 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
> >
>
> --
> Dr Jane Aspell Department of Experimental Psychology, University of
> Oxford, South Parks Road, Oxford, OX1 3UD tel: +44 (0)1865-281606
>
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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