Vizualisation, niBabel error, deprecated

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Dear all,
I have a following issue
When I use e.g,
mne.viz.plot_bem(subject=subject, subjects_dir=subjects_dir,
                 brain_surfaces='white', orientation='coronal')
I get now following output with errors errors:
Using surface:
C:/Users/ekirl/OneDrive/Documents/MNE/mri/04SMFS\bem\inner_skull.surf
Using surface:
C:/Users/ekirl/OneDrive/Documents/MNE/mri/04SMFS\bem\outer_skull.surf
Using surface:
C:/Users/ekirl/OneDrive/Documents/MNE/mri/04SMFS\bem\outer_skin.surf
C:\Users\ekirl\Anaconda3\lib\site-packages\mne\viz\misc.py:307:
DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which
has a more predictable return type. To obtain get_data() behavior going
forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of
version: 5.0
  data = nim.get_data()
Traceback (most recent call last)
etc...

What can be done here?

I use mne 19.0.2, niBabel 3.0.0, Python 3.7.2
The same error on both Mac and Windows
Thank you in advance.
Sincerely yours,
Kirill Elin
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it's a deprecation warning not really an error.

MNE 0.20 will capture this warning.

Alex

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Thank you!
So what is the error then?
The bem files are correct and the figure is produced on Ubuntu machine.
When copied to windows, I get then the following error:
mne.viz.plot_bem(subject=subject, subjects_dir=subjects_dir,
                 brain_surfaces='white', orientation='coronal')
Using surface:
C:/Users/ekirl/OneDrive/Documents/MNE/mri/04SMFS\bem\inner_skull.surf
Using surface:
C:/Users/ekirl/OneDrive/Documents/MNE/mri/04SMFS\bem\outer_skull.surf
Using surface:
C:/Users/ekirl/OneDrive/Documents/MNE/mri/04SMFS\bem\outer_skin.surf
Traceback (most recent call last):

  File "<ipython-input-19-f01509936b0d>", line 2, in <module>
    brain_surfaces='white', orientation='coronal')

  File "C:\Users\ekirl\Anaconda3\lib\site-packages\mne\viz\misc.py", line
470, in plot_bem
    show)

  File "C:\Users\ekirl\Anaconda3\lib\site-packages\mne\viz\misc.py", line
330, in _plot_mri_contours
    surf['rr'], surf['tris'] = read_surface(file_name)

  File
"<C:\Users\ekirl\Anaconda3\lib\site-packages\mne\externals\decorator.py:decorator-gen-39>",
line 2, in read_surface

  File "C:\Users\ekirl\Anaconda3\lib\site-packages\mne\utils\_logging.py",
line 90, in wrapper
    return function(*args, **kwargs)

  File "C:\Users\ekirl\Anaconda3\lib\site-packages\mne\surface.py", line
657, in read_surface
    ret = _get_read_geometry()(fname, read_metadata=read_metadata)

  File
"C:\Users\ekirl\Anaconda3\lib\site-packages\nibabel\freesurfer\io.py", line
185, in read_geometry
    raise ValueError("File does not appear to be a Freesurfer surface")

ValueError: File does not appear to be a Freesurfer surface

Thank you in advance.
Sincerely yours,
Kirill

??, 4 ???. 2020 ?. ? 23:20, Alexandre Gramfort <alexandre.gramfort at inria.fr

:

        External Email - Use Caution

it's a deprecation warning not really an error.

MNE 0.20 will capture this warning.

Alex

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