[Mne_analysis] Problem reading competition data

[Vladimir Litvak]

        External Email - Use Caution        

Sorry, my mistake. The command and the error are below.

Thanks,

Vladimir


In [117]: bem_file=subject+'-bem.fif'

     ...:

     ...: if op.isfile(bem_file):

     ...: bem = mne.read_bem_surfaces(bem_file)

     ...: else:

     ...: bem = mne.make_bem_model(mri_dir)

     ...: mne.write_bem_surfaces(bem_file, bem)

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 0.90 -5.99 -0.58 mm

outer skull CM is 0.90 -5.96 -1.02 mm

inner skull CM is 0.85 -6.62 6.36 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 "<ipython-input-117-e6e8d7e63470>", line 6, in <module>

bem = mne.make_bem_model(mri_dir)


File "<string>", line 2, in make_bem_model


File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/utils.py",
line 729, in verbose

return function(*args, **kwargs)


File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 572, in make_bem_model

surfaces = _surfaces_to_bem(surfaces, ids, conductivity, ico)


File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 502, in _surfaces_to_bem

_check_surfaces(surfs, incomplete=incomplete)


File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 443, in _check_surfaces

_assert_inside(surf_2, surf_1)


File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 432, in _assert_inside

% (_surf_name[fro['id']], _surf_name[to['id']]))


RuntimeError: Surface inner skull is not completely inside surface outer skull
On Fri, Jun 22, 2018 at 1:49 PM Alexandre Gramfort
<alexandre.gramfort at m4x.org> wrote:
>
>         External Email - Use Caution
>
> sorry I don't see the error.
>
> btw it must work as we have played with these data successfully.
>
>
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