hi stephen
i've uploaded tarred and zipped directories for the gfeat and one first level
feat to /usr/fs5/aspell/FSList on cayenne.
is the problem that even though the option in the higher level analysis is
'first highres' this has somehow been transformed into standard space (and
consequently look distorted) because the higher level analysis is really
designed to combine data from different subjects, not different sessions for the
same subject? (which would also explain why my z scores go down when i combine
the first level feats - a mixed effects analysis is being carried out, whereas
since all the lower level feats are from the same subject, i should be doing a
fixed effects analysis?)
thanks
jane
In message <[log in to unmask]> FSL
- FMRIB's Software Library <[log in to unmask]> writes:
> Hi Jane - did you find the problem with this? If the first-level
> registrations look fine but the second-level results look like they have
> registration issues then something strange is going on - if you create a
> tarfile of the gfeat and an example first-level feat we can look into
> this. if you put the tarfile on a web/ftp site we can download and look.
>
> Cheers.
>
>
> On Tue, 9 Mar 2004, Jane Aspell wrote:
>
> > hi stephen
> >
> > yes - they all seem fine.
> >
> > jane
> >
> >
> > In message <[log in to unmask]> FSL
> > - FMRIB's Software Library <[log in to unmask]> writes:
> > > Hi - there may be a few things going on here. Could you start by looking
> > > at the registration report page for each first-level analysis (click on
> > > the summary registration overlay image towards the bottom of the
> > > first-level FEAT output web page). Do all stages look like they worked ok?
> > >
> > > Cheers.
> > >
> > >
> > >
> > > On Mon, 8 Mar 2004, Jane Aspell wrote:
> > >
> > > > Hi
> > > >
> > > > Thanks for all the previous help. I've a question about rendering in higher
> > > > level analysis...my lower level feat directories are all from a single
> > > > subject and in the higher level analysis i want to render the activations
> > > > onto the high res structural image for this subject. i chose the render onto
> > > > 'first highres' option as i thought that would achieve this. when i open the
> > > > resulting 'rendered_threshzstat1.hdr' for example, it seems that is has used
> > > > the correct image but it looks distorted - the frontal and occipital cortex
> > > > look squashed. the image also looks blurred.
> > > > i wanted to overlay some masks i have from a retinotopic scan onto the high
> > > > res image showing activations. the masks show the location of the lower
> > > > visual areas and they normally overlay onto the same sturctural image that i
> > > > selected for the higher level analysis but i am not able to put together the
> > > > high res, the activations and the masks at once -'cannot load incompatible
> > > > overlay'.
> > > > can you explain why the subject's high res seems to have been distorted by
> > > > the higher level analysis and why i can't overlay my masks onto the highres
> > > > image showing activations?
> > > >
> > > > thanks very much
> > > >
> > > > 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
>
--
Dr Jane Aspell
Department of Experimental Psychology, University of Oxford,
South Parks Road, Oxford, OX1 3UD
tel: +44 (0)1865-281606
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