[Mne_analysis] problem with setting up the source space

[Lin Wang]

Hi Eric,

Thanks for your quick response!

I used ico5 to have a better spatial resolution. I saw several other papers
used this setting.

I quickly checked five participants. Indeed it seems that these two
subjects have smaller brain than others.

But I still don't understand why the higher resolution causes this error. I
thought the smaller spacing should result in more neighbors...

Thanks again for  your help!

Lin



On Mon, May 22, 2017 at 2:57 PM, Eric Larson <larson.eric.d at gmail.com>
wrote:

> 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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