[FieldTrip] freesurfer surfaces

[Gio Piantoni]

I fixed the "Arlecchino brain" problem and committed the patch
(r6433). I'd still appreciate if people had some suggestions about the
analysis steps for the group-average.

Best,

Gio

On Wed, Sep 5, 2012 at 10:20 AM, Gio Piantoni <g.piantoni at nin.knaw.nl> wrote:
> Dear Fieldtrip developers,
>
> I'd like to run source reconstruction on the cortical sheets obtained
> from Freesurfer and average them using the "sphere" approach of
> Freesurfer. I have these steps in mind:
>
> 1) create a 3-layer BEM ('outer_skin' 'inner_skull'  'brain' from the
> bem/watershed folder, which I think might be better than 'outer_skin'
> 'outer_skull' 'inner_skull' as in
> http://fieldtrip.fcdonders.nl/development/replicate_functionality_of_mne_software
> )
> 2) create a forward model from a subset of points in "?h.smoothwm"
> (for computational purposes)
> 3) do source reconstruction on this subset of dipoles
> 4) source interpolate to the high resolution of ?h.smoothwm
> 5) project all the locations onto the ?h.sphere
> 6) interpolate to the points to the ?h.sphere of fsaverage
> 7) do 2-D statistics on the values of the ?h.sphere of fsaverage (and
> plot them using ?h.inflated of fsaverage)
>
> I was wondering if anybody has tried something similar and if there
> are steps I should be careful about. There was a discussion in
> January/February about doing statistics on cortical sheets:
> http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004749.html
> http://mailman.science.ru.nl/pipermail/fieldtrip/2012-February/004766.html
>
> Does anybody have suggestions about these steps? I promise I'll make a
> tutorial out of this, if it works out ;)
>
> A practical point I get stuck in is at steps 3) and 4). The
> interpolation from a subset of 2-D points to another subset of 2-D
> points gives a bit of nonsensical results. Code:
>
> %-get freesurfer surface
> bnd = ft_read_headshape('lh.smoothwm');
> % get it from https://skydrive.live.com/redir?resid=6D9DCA0F726A645C!7000
> % or any freesurfer surface you have
>
> %-downsample
> bnd_down = bnd;
> P.faces = bnd_down.tri;
> P.vertices = bnd_down.pnt;
> P = reducepatch(P, 0.05);
> bnd_down.tri = P.faces;
> bnd_down.pnt = P.vertices;
>
> %-create source
> source.pos = bnd_down.pnt;
> source.inside = true(size(source.pos,1),1);
> source.pow = bnd_down.pnt(:,3); % "fake" source reconstruction
>
> figure
> ft_plot_mesh(bnd_down, 'edgecolor', 'none', 'vertexcolor', source.pow)
> % the rainbow brain
> view(90, 0); camlight
>
> %-sourceinterpolate
> cfg = [];
> cfg.parameter = 'pow';
> ana = [];
> ana.pnt = bnd_down.pnt;
> ana.orig = bnd;
> souinterp = ft_sourceinterpolate(cfg, source, ana);
>
> figure
> ft_plot_mesh(souinterp, 'edgecolor', 'none', 'vertexcolor',
> souinterp.pow) % the Arlecchino brain
> view(90, 0); camlight
>
> Should I file a bugzilla report for this? I haven't done it as I'm not
> even sure this is the correct input format.
> Thanks for any suggestion.
>
> Best wishes,
>
> Gio
>
> --
> Giovanni Piantoni, MSc
> Dept. Sleep & Cognition
> Netherlands Institute for Neuroscience
> Meibergdreef 47
> 1105 BA Amsterdam (NL)
> www.gpiantoni.com