thanks steve
my problem was aligning masks of visual areas to the highres showing activations
but i think i've fixed that now.
so is it because my registration is not very robust that my highres brain looks
distorted in shape after going through higher level feat?
jane
In message <[log in to unmask]>
FSL - FMRIB's Software Library <[log in to unmask]> writes:
> Thanks. A few things:
>
> You might get more robust registration for the "initial structural image"
> if you use 6DOF (though these results look fine) or even 3DOF IF the
> initial structural contains identical data to the FMRI data (ie doesn't
> need any rotations to get good alignment).
>
> I'm confused as to why you're worried about the gfeat pictures overlaid
> onto the highres - they look fine to me! Which aspects worried you?
>
> You're right that the mixed-effects analysis carried out by the
> higher-level FEAT will reduce the Z-scores from the first-levels in
> general. However, you are getting lots of nice activation. But yes, if you
> just want to summarise this subject's data you might want to use FE
> instead (see the email list for how to do this).
>
> Cheers, Steve.
>
>
>
>
> On Thu, 18 Mar 2004, Jane Aspell wrote:
>
> > 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
> >
>
> 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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