[Mne_analysis] Identifying adjacent sources
Alexandre Gramfort
gramfort at nmr.mgh.harvard.edu
Sun May 12 09:22:38 EDT 2013
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
HTH
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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