[Mne_analysis] Identifying adjacent sources

[Alexandre Gramfort]

hi Steve,

> 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?

yes exactly.

> 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...

very good questions. I usually use fsaverage but I guess the answer is yes you
should setup a source space for the average brain.

HTH
Alex