[Mne_analysis] Conductivity 1 layer or 3
Alexandre Gramfort
alexandre.gramfort at inria.fr
Mon Apr 6 11:22:06 EDT 2020
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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
On Mon, Apr 6, 2020 at 11:43 AM Andrade Rey René
<rene.andrade at edu.uah.es> wrote:
>
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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
>
> 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:
>
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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> 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> 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> 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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