[Mne_analysis] Identifying adjacent sources

Stephen Politzer-Ahles politzerahless at gmail.com
Mon May 13 19:50:30 EDT 2013
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Hi Alexandre,

Thanks for the information. I think I've figured out how to get the source
space with triangulation now (after playing around, I found that in
addition to using the --ico option when running *mne_setup_forward_model*,
when running *mne_do_forward_solution* I also had to use the --src option
to pick out the "<subject>-ico-4-src.fif" source space rather than whatever
it was picking out by default). But now I have two related questions about
my workflow:

Firstly, I am actually computing my source estimates (.stc files) morphed
to one brain. So does that mean that, when figuring out the vertex info
using these functions, I should be using the forward solution for the brain
to which everyone else's was morphed, rather than using each individual
subject's forward solution?

And a related question: so far I have mostly been doing source estimates
morphed to an average brain (using *make_average_subject*, then *
mne_make_morph_maps*, then using the --morph option with *mne_make_movie*).
But I never set up a forward model for the averaged brain (i.e. I didn't
run mne_setup_forward_model or mne_do_forward_solution on that brain); is
that the correct way to do it? Obviously if I didn't set up a forward model
for the averaged brain then I can't use mne.read_forward_solution to get
out the triangles in Python...but I suppose I could just re-do the analysis
and morph the data to some random subject who *does* have a forward model
set up, rather than the average brain, and then I'd be able to do that.

Thanks for your help!

On Sun, May 12, 2013 at 8:22 AM, Alexandre Gramfort <
gramfort at nmr.mgh.harvard.edu> wrote:

> hi Stephen,
> if you use an ico or oct source space you have the triangles for the source
> space from which you can extract the adjacency matrix.
> See :
> http://martinos.org/mne/auto_examples/plot_read_forward.html#example-plot-read-forward-py
> for how to access the use_tris in Python (should be the same in matlab)
> and the mesh_edges function:
> https://github.com/mne-tools/mne-python/blob/master/mne/source_estimate.py#L1419
> Alex
> On Sat, May 11, 2013 at 12:09 PM, A.C.G. Thwaites <acgt2 at cam.ac.uk> wrote:
> > Hi Steve,
> >
> > I have a function for this, it accepts a .surf mesh, a center vertex
> > number, and a 'distance' d and it returns a list of vertices d vertices
> > away from the centre vertex (so distance 1 would return a list of every
> > vertex adjacent to the centre vertex, distance 2 would be the vertices
> that
> > form a ring around the adjacent vertices, etc).
> >
> > I can't remember if it does the full mesh or allows you to search
> through a
> > downsampled mesh (ie just the sources you have estimated).
> >
> > I'll check and send it to the list on monday.
> >
> > Andy
> >
> >
> >
> >
> > On May 11 2013, Stephen Politzer-Ahles wrote:
> >
> >>Hello,
> >>
> >>Is there a straighforward method to figure out, for any cortical source
> or
> >>vertex, what the adjacent cortical sources/vertices are?
> >>
> >>More specifically, I have extracted .amp timecourse files for each
> >>participant and condition that look something like this:
> >>    100779 9.76119e-13 9.8006e-13 1.01097e-12 1.0584e-12
> >>    102810 5.77402e-13 4.74985e-13 6.13183e-13 8.53066e-13
> >>    103338 7.69642e-13 1.13359e-12 1.48948e-12 1.78157e-12
> >>    103374 6.44688e-13 8.72736e-13 1.09166e-12 1.24282e-12
> >>where the first number in each row is the vertex that timecourse comes
> from
> >>(and the following columns are the current estimates at each timepoint).
> >>I'm interested in doing a permutation-based spatiotemporal clustering
> test,
> >>so what I'd like to be able to do is, for each of those vertices, to get
> a
> >>list of which sources are adjacent to it. (Not necessarily which vertices
> >>are adjacent to it, since my understanding is that the cortical sources
> >>represent just a subset of the vertices present in the original
> >>tesselation.) I assume that after triangulation there must be some record
> >>of this, or some way to find it out, but I can't figure out where to find
> >>it. By the way, my structural images were segmented in Freesurfer, so the
> >>triangulations are in .surf files rather than .tri files.
> >>
> >>Any advice is greatly appreciated! Thank you,
> >>Steve Politzer-Ahles
> >>
> >>
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Stephen Politzer-Ahles
University of Kansas
Linguistics Department
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