[Mne_analysis] Conductivity 1 layer or 3

Andrade Rey René rene.andrade at edu.uah.es
Mon Apr 6 11:29:09 EDT 2020
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if there is any problem in mri segmentation what can I do? 

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> On 6 Apr 2020, at 17:23, Alexandre Gramfort <alexandre.gramfort at inria.fr> wrote:
> 
>         External Email - Use Caution        
> 
> I think the error is pretty clear:
> 
> RuntimeError: Surface inner skull is not completely inside surface outer skull
> 
> forward model requires nested compartments. Use plot_bem to check the quality
> of the MRI segmentation
> 
> HTH
> A
> 
>> On Mon, Apr 6, 2020 at 11:43 AM Andrade Rey René
>> <rene.andrade at edu.uah.es> wrote:
>> 
>>        External Email - Use Caution
>> 
>> Sorry it is not fixed!! It says the same error
>> 
>> 
>>>>> model = mne.make_bem_model(subject='bert', ico=5,
>> ...                            conductivity=conductivity,
>> ...                            subjects_dir='/usr/local/freesurfer/subjects/')
>> Creating the BEM geometry...
>> Going from 5th to 5th subdivision of an icosahedron (n_tri: 20480 -> 20480)
>> Going from 5th to 5th subdivision of an icosahedron (n_tri: 20480 -> 20480)
>> Going from 5th to 5th subdivision of an icosahedron (n_tri: 20480 -> 20480)
>> outer skin  CM is   0.61 -19.22   0.35 mm
>> outer skull CM is   0.63 -19.11  -0.15 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
>> 
>> On 6 Apr 2020, at 11:38, Andrade Rey René <rene.andrade at edu.uah.es> wrote:
>> 
>>>>> 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> wrote:
>> 
>>       External Email - Use Caution
>> 
>> 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> wrote:
>> 
>> 
>>       External Email - Use Caution
>> 
>> 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> wrote:
>> 
>>         External Email - Use Caution
>> 
>> 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> wrote:
>> 
>>      External Email - Use Caution
>> 
>> 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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