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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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hi,
if you have EEG you must use 3 layers.
The 1 layer option is just for MEG.
HTH
Alex
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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!!
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yes a full print of the error can help.
A
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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?
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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
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?
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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
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if there is any problem in mri segmentation what can I do?
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See
https://mne.tools/dev/overview/faq.html#my-watershed-bem-meshes-look-incorrect
Eric