[Mne_analysis] issue with brainsuite and bem ico_downsample

[Eric Larson]

        External Email - Use Caution        

The error is in the downsampling step (we should probably improve the
message). Set `ico=None` and it won't try to downsample your surface:

https://martinos.org/mne/stable/generated/mne.make_bem_model.html

It would be good indeed to see how this works with sample data and see if
it affects source localization -- feel free to open an MNE issue about that.

Eric


On Fri, Apr 5, 2019 at 4:32 AM Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:

>         External Email - Use Caution
>
> hi Yvonne,
>
> I've never tried this route to BEM model generation. Can you do this
> procedure with
> MNE sample dataset and share with us the generate .surf files so we can
> replicate
> and hopefully fix the pb?
>
> ALex
>
> On Fri, Apr 5, 2019 at 1:16 AM Yvonne Yau <yvonne.yau at mail.mcgill.ca>
> wrote:
>
>>         External Email - Use Caution
>>
>> ​Hi guys,
>> I'm having some issues with the BEM meshes for my EEG data.  I've tried
>> two approaches:
>> (1) Using freesurfer watershed and trying different preflood levels, but
>> it seems to do a bad job with the outer_skull.surf being misplaced (see
>> attached image)
>> (2) I've had better success with using Brainsuite and have followed the
>> guidelines; converting it from dfs to surf using mne_convert_surface, and
>> then reducing the number of triangles to 10,000 using mne_reduce_surface.
>> When I try to run mne.make_bem_mode, I get the error:
>> File "/usr/anaconda3/envs/mne/lib/python3.6/site-packages/mne/bem.py",
>> line 344, in _ico_downsample
>>
>> raise RuntimeError(bad_msg)
>>
>>
>> RuntimeError: A surface with 10000 triangles cannot be isomorphic with a
>> subdivided icosahedron.
>>
>> Any ideas?
>>
>> Best, Yvonne
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