[Mne_analysis] issue with brainsuite and bem ico_downsample

Sat Apr 6 18:27:16 EDT 2019

        External Email - Use Caution        

Ahh I see that they are in the GitHub issue. I'll take a look next week if
nobody beats me to it.

Eric

On Sat, Apr 6, 2019, 18:23 Eric Larson <larson.eric.d at gmail.com> wrote:

> That divide by zero is probably the problem and might be fixable. Can you
> share the surfaces on DropBox or some other file hosting service?
>
> Eric
>
> On Sat, Apr 6, 2019, 14:01 Yvonne Yau <yvonne.yau at mail.mcgill.ca> wrote:
>
>>         External Email - Use Caution
>>
>> I opened an MNE issue for the downsampling problem (
>> https://github.com/mne-tools/mne-python/issues/6127)
>>
>>
>>
>> When I set the ico=None, I run into a new issue with
>> mne.make_bem_solution after mne.make_bem_model.  I don't get this issue
>> with the MNE sample dataset but with my acquired T1's.  Any ideas?  Thanks
>> for your help guys.
>>
>> bem = mne.make_bem_solution(surfaces, verbose='INFO')
>>
>> Approximation method : Linear collocation
>>
>> Three-layer model surfaces loaded.
>>
>> Computing the linear collocation solution...
>>
>> Matrix coefficients...
>>
>> head (5002) -> head (5002) ...
>>
>> /dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/mne/bem.py:151:
>> RuntimeWarning: divide by zero encountered in double_scalars
>>
>> miss /= (4.0 * n_memb)
>>
>> head (5002) -> outer_skull (5002) ...
>>
>> head (5002) -> inner_skull (5002) ...
>>
>> outer_skull (5002) -> head (5002) ...
>>
>> outer_skull (5002) -> outer_skull (5002) ...
>>
>> outer_skull (5002) -> inner_skull (5002) ...
>>
>> inner_skull (5002) -> head (5002) ...
>>
>> inner_skull (5002) -> outer_skull (5002) ...
>>
>> inner_skull (5002) -> inner_skull (5002) ...
>>
>> Inverting the coefficient matrix...
>>
>> Traceback (most recent call last):
>>
>>
>> File "<ipython-input-18-24943e2f3a65>", line 1, in <module>
>>
>> bem = mne.make_bem_solution(surfaces, verbose='INFO')
>>
>>
>> File
>> "</dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/mne/externals/decorator.py:decorator-gen-39>",
>> line 2, in make_bem_solution
>>
>>
>> File
>> "/dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/mne/utils/_logging.py",
>> line 88, in wrapper
>>
>> return function(*args, **kwargs)
>>
>>
>> File
>> "/dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/mne/bem.py",
>> line 326, in make_bem_solution
>>
>> _fwd_bem_linear_collocation_solution(bem)
>>
>>
>> File
>> "/dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/mne/bem.py",
>> line 267, in _fwd_bem_linear_collocation_solution
>>
>> m['solution'] = _fwd_bem_multi_solution(coeff, m['gamma'], nps)
>>
>>
>> File
>> "/dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/mne/bem.py",
>> line 225, in _fwd_bem_multi_solution
>>
>> return linalg.inv(solids, overwrite_a=True)
>>
>>
>> File
>> "/dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/scipy/linalg/basic.py",
>> line 945, in inv
>>
>> a1 = _asarray_validated(a, check_finite=check_finite)
>>
>>
>> File
>> "/dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/scipy/_lib/_util.py",
>> line 239, in _asarray_validated
>>
>> a = toarray(a)
>>
>>
>> File
>> "/dagher/dagher6/yyau/toolbox/anaconda3/envs/mne/lib/python3.6/site-packages/numpy/lib/function_base.py",
>> line 498, in asarray_chkfinite
>>
>> "array must not contain infs or NaNs")
>>
>>
>> ValueError: array must not contain infs or NaNs
>>
>>
>> ------------------------------
>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
>> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Eric Larson <
>> larson.eric.d at gmail.com>
>> *Sent:* April 5, 2019 9:54 AM
>> *To:* Discussion and support forum for the users of MNE Software
>> *Subject:* Re: [Mne_analysis] issue with brainsuite and bem
>> ico_downsample
>>
>>
>>         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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