nope - your highres _doesn't_ look distorted! It has been transformed into
standard space and looks fine.
Cheers :)
On Thu, 18 Mar 2004, Jane Aspell wrote:
> 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
>
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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