Hi Hauke,
Do you mean the simple single Gamma HRF? The code for generating the
design matrix given the user specification is in
stable-src/feat5/feat_model.c
the time series for some of the plots are averaged over all "activated"
voxels; by default a voxel's time series contributes to the mean according
to it's Z value - you can turn that off for flat weighting.
I think flame should just work already on Freesurfer-generated group
files?
ttfn :)
On Fri, 18 Apr 2003, Hauke Heekeren wrote:
> Hi there,
> 3 quick questions
>
> - how exactly do you guys compute the hrf in the case of using a gamma
> variate and where in the source code can we find it?
>
> - when using tsplot what's the effect of using "-n" (don't weight
> cluster averaging with Z stats)
>
> - stats on the surface: is there a way to use flame (instead of OLS) on
> sphere registered data?
>
> thanks,
>
> h.
>
>
> >
> >
> >
> >
>
> -
> >Do FEAT statistics on these "spherical standard space" files (left and
> right hemispheres >separately).
> >For the moment can do random effects stats on the copes using avwmaths;
> the nearly-ready >FEAT5 will make this easy for you...watch this space.
> >On Fri, 2003-04-18 at 04:52, Stephen Smith wrote:
>
> > Thanks Darren. Also, Ed, there is a page explicitly about using FSL and
> > FreeSurfer together to do the kind of thing you are asking about.
> >
> > http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
> >
> > Personally, I think FreeSurfer is excellent both as research and software.
> >
> > Thanks, Steve.
> >
> >
> >
> > On Fri, 18 Apr 2003, Darren Weber wrote:
> >
> > > Hi Ed,
> > >
> > > you can map fMRI analysis results onto a cortical surface using freesurfer.
> > > If you do individual subject fMRI analysis, then map the result to the
> > > individual subject cortex (assuming the results are on or near that
> > > surface), then you can use freesurfer to perform group surface averages and
> > > statistics. These analyses are not in Talairach space, but there are
> > > surface morphing routines in freesurfer that will align the cortical surface
> > > gyri/sulci across subjects. See the freesurfer website and email archives
> > > for further info or post email to that discussion list.
> > >
> > > Regards, Darren
> > >
> > >
> > > ----- Original Message -----
> > > From: "Edward Vessel" <[log in to unmask]>
> > > To: <[log in to unmask]>
> > > Sent: Friday, April 18, 2003 10:07 AM
> > > Subject: [FSL] freesurfer
> > >
> > >
> > > > Hi folks -
> > > >
> > > > given the upcoming course on FSL and freesurfer, I am assuming that the
> > > two
> > > > are somewhat compatible. However, I can't imagine how one would go about
> > > > doing a higher level (cross subject) analysis on a flat map dataset in
> > > FSL.
> > > > I thought FSL could only take in images in analyze format. How would one
> > > go
> > > > about doing this?
> > > >
> > > > By the way ... I am considering this as an option since my attempts to
> > > weight
> > > > the affine transform to standard space for particular areas of interest
> > > has
> > > > yet to yield decent results.
> > > >
> > > > thanks,
> > > > Ed
> > > >
> > > > --
> > > > Ed Vessel
> > > > U. of Southern California [log in to unmask]
> > > > Dept. of Neuroscience
> > > > HNB, 3641 Watt Way http://geon.usc.edu/~vessel
> > > > Los Angeles, CA 90089-2520
> > > > (213) 740-6102
> > > >
> > >
> >
> > Stephen M. Smith MA DPhil CEng MIEE
> > 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
>
Stephen M. Smith MA DPhil CEng MIEE
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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