[Mne_analysis] Conductivity 1 layer or 3

[Andrade Rey René]

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>>> conductivity = (0.3, 0.006, 0.3)
>>> model = mne.make_bem_model(subject='bert', ico=4,
...                            conductivity=conductivity,
...                            subjects_dir='/usr/local/freesurfer/subjects/')
Creating the BEM geometry...
Going from 5th to 4th subdivision of an icosahedron (n_tri: 20480 -> 5120)
Going from 5th to 4th subdivision of an icosahedron (n_tri: 20480 -> 5120)
Going from 5th to 4th subdivision of an icosahedron (n_tri: 20480 -> 5120)
outer skin  CM is   0.61 -19.22   0.36 mm
outer skull CM is   0.63 -19.11  -0.14 mm
inner skull CM is   0.02 -21.14   9.57 mm
Checking that outer skull surface is inside outer skin  surface...
Checking that inner skull surface is inside outer skull surface...
Traceback (most recent call last):
  File "<stdin>", line 3, in <module>
  File "<decorator-gen-72>", line 21, in make_bem_model
  File "/home/andraderenew/.local/lib/python3.7/site-packages/mne/bem.py", line 590, in make_bem_model
    surfaces = _surfaces_to_bem(surfaces, ids, conductivity, ico)
  File "/home/andraderenew/.local/lib/python3.7/site-packages/mne/bem.py", line 523, in _surfaces_to_bem
    _check_surfaces(surfs, incomplete=incomplete)
  File "/home/andraderenew/.local/lib/python3.7/site-packages/mne/bem.py", line 462, in _check_surfaces
    _assert_inside(surf_2, surf_1)
  File "/home/andraderenew/.local/lib/python3.7/site-packages/mne/bem.py", line 451, in _assert_inside
    % (_surf_name[fro['id']], _surf_name[to['id']]))
RuntimeError: Surface inner skull is not completely inside surface outer skull


With "ico = 5” it is fixed what is the idea behind this behavior?

On 5 Apr 2020, at 21:29, Alexandre Gramfort <alexandre.gramfort at inria.fr<mailto:alexandre.gramfort at inria.fr>> wrote:

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yes a full print of the error can help.

A

On Fri, Apr 3, 2020 at 10:10 AM Andrade Rey René
<rene.andrade at edu.uah.es<mailto:rene.andrade at edu.uah.es>> wrote:

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Do you need me to show you the error or do you already have an idea of the issue that I have when doing the conductivity with 3 layers in bem model? I don't remember what it said but there was certainly an error stoping me from going further in the analysis. I used the numbers in conductivities from a tutorial in mne. I don't know if these numbers change and how to obtain them.
Thanks!!

Sent from my iPhone

On 3 Apr 2020, at 09:24, Alexandre Gramfort <alexandre.gramfort at inria.fr<mailto:alexandre.gramfort at inria.fr>> wrote:

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hi,

if you have EEG you must use 3 layers.

The 1 layer option is just for MEG.

HTH
Alex

On Thu, Apr 2, 2020 at 11:31 PM Andrade Rey René
<rene.andrade at edu.uah.es<mailto:rene.andrade at edu.uah.es>> wrote:

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Dear experts:

There is an issue I don´t know how to proceed with. I am trying to do forward solution and I need  to have made BEM model for which I need to introduce conductivity defined for 1 or 3 layers. If I do 3 the output is an error if I choose 1 layer the output in forward solution is an error pointing to 3 layers in BEM model. What can I do?

Sincerely,
Andrade.

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