[Mne_analysis] Conductivity 1 layer or 3

Eric Larson larson.eric.d at gmail.com
Mon Apr 6 11:38:12 EDT 2020
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See
https://mne.tools/dev/overview/faq.html#my-watershed-bem-meshes-look-incorrect

Eric


On Mon, Apr 6, 2020 at 11:29 AM Andrade Rey René <rene.andrade at edu.uah.es>
wrote:

>         External Email - Use Caution
>
> if there is any problem in mri segmentation what can I do?
>
> Sent from my iPhone
>
> > 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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> >>
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