[Mne_analysis] problem with setting up the source space

[Eric Larson]

In lieu of a better (code) fix, I'd use the default oct6 spacing. Is there
a reason you prefer ico5?

Do these subjects have particularly small heads by any chance?

Eric


On Mon, May 22, 2017 at 2:51 PM, Lin Wang <wanglinsisi at gmail.com> wrote:

> Hi all,
>
> I got the following error when creating the source space with
> mne.setup_source_space(). The spacing was set to 'ico5'.
>
> *Triangle file: created by lw604 on Sat Dec  3 16:57:00 2016 nvert =
> 145568 ntri = 291132*
> *Mapping lh 08_NonCon -> ico (5) ...*
> *    Source space vertex moved from 145214 to 145216 because of double
> occupation*
> *    Source space vertex moved from 56257 to 56268 because of double
> occupation*
> *    Source space vertex moved from 56268 to 145227 because of double
> occupation*
> *    Source space vertex moved from 145227 to 57616 because of double
> occupation*
> *Traceback (most recent call last):*
> *  File "<stdin>", line 3, in <module>*
> *  File "<string>", line 2, in setup_source_space*
> *  File
> "/autofs/cluster/kuperberg/nonconMM/MEG/python/anaconda/lib/python2.7/site-packages/mne/utils.py",
> line 708, in verbose*
> *    return function(*args, **kwargs)*
> *  File
> "/autofs/cluster/kuperberg/nonconMM/MEG/python/anaconda/lib/python2.7/site-packages/mne/source_space.py",
> line 1311, in setup_source_space*
> *    subjects_dir)*
> *  File
> "/autofs/cluster/kuperberg/nonconMM/MEG/python/anaconda/lib/python2.7/site-packages/mne/surface.py",
> line 677, in _create_surf_spacing*
> *    '%d / %d' % (k, nmap))*
> *RuntimeError: Could not find neighbor for vertex 8590 / 10242*
>
> I have completed the cortical surface reconstruction with FreeSurfer.
> Also, there was no error when I set spacing = 'oct6'.
>
> We have 32 participants, and only two participants have this type of
> error. What should I do?
>
> Thanks for your help!
>
> Lin
>
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