Hi!
I have been using MNE to perform the pre-processing of my MEG data. As we’re working in a group, we are using a Jupyter Notebook edited on VisualStudio to run the analyses.
We managed to run the co-registration via IPython directly in bash, but I was looking into adding this step into the notebook, and encountered one error.
Here is the complete code I have:
# Imports
import os
import os.path as op
import mne
# Variables
output_path = 'MEGtrain/'
fs_subject = "fs-06"
subjects_dir = op.join(output_path, 'fs/')
os.environ["SUBJECTS_DIR"] = subjects_dir
# Create head-dense.fif file (this works)
mne.bem.make_watershed_bem(subject = fs_subject, overwrite = True)
mne.bem.make_scalp_surfaces(subject = fs_subject, overwrite = True, force = True)
# Display the hemispheres (this does not work)
Brain = mne.viz.get_brain_class() # Create a Brain object
brain = Brain(subject,
hemi = 'both', # The hemisphere to visualize (`lh`, `rh`, `both`, or `split`)
subjects_dir = subjects_dir,
size = (800, 600) # The size of the window in pixels
)
brain.add_annotation('aparc.a2009s', borders = False)
brain.add_head(dense = True)
# Co-registration (this does not work)
mne.gui.coregistration(subject = fs_subject, subjects_dir = subjects_dir)
After trying to create the brain object or performing the co-registration, I get this error message:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[6], line 2
1 Brain = mne.viz.get_brain_class() # Create a Brain object
----> 2 brain = Brain(subject,
3 hemi = 'both', # The hemisphere to visualize (`lh`, `rh`, `both`, or `split`)
4 subjects_dir = subjects_dir,
5 size = (800, 600) # The size of the window in pixels
6 )
7 brain.add_annotation('aparc.a2009s', borders = False)
8 brain.add_head(dense = True)
File /megtrain_env/.conda/lib/python3.10/site-packages/mne/viz/_brain/_brain.py:409, in Brain.__init__(***failed resolving arguments***)
407 logger.debug(f"Hemi offset: {offset}")
408 _validate_type(theme, (str, None), "theme")
--> 409 self._renderer = _get_renderer(
410 name=self._title, size=size, bgcolor=self._bg_color, shape=shape, fig=figure
411 )
412 self._renderer._window_close_connect(self._clean)
413 self._renderer._window_set_theme(theme)
File /megtrain_env/.conda/lib/python3.10/site-packages/mne/viz/backends/renderer.py:57, in _get_renderer(*args, **kwargs)
55 def _get_renderer(*args, **kwargs):
56 _get_3d_backend()
---> 57 return backend._Renderer(*args, **kwargs)
File /megtrain_env/.conda/lib/python3.10/site-packages/mne/viz/backends/_notebook.py:1561, in _Renderer.__init__(self, *args, **kwargs)
1555 if not _notebook_vtk_works():
1556 raise RuntimeError(
1557 "Using the notebook backend on Linux requires a compatible "
1558 "VTK setup. Consider using Xfvb or xvfb-run to set up a "
1559 "working virtual display, or install VTK with OSMesa enabled."
1560 )
-> 1561 super().__init__(*args, **kwargs)
1562 self._window_initialize(fullscreen=fullscreen)
File /megtrain_env/.conda/lib/python3.10/site-packages/mne/viz/backends/_pyvista.py:269, in _PyVistaRenderer.__init__(self, fig, size, bgcolor, name, show, shape, notebook, smooth_shading, splash, multi_samples)
266 # pyvista theme may enable depth peeling by default so
267 # we disable it initially to better control the value afterwards
268 with _disabled_depth_peeling():
--> 269 self.plotter = self.figure._build()
270 self._hide_axes()
271 self._toggle_antialias()
File /megtrain_env/.conda/lib/python3.10/site-packages/mne/viz/backends/_pyvista.py:161, in PyVistaFigure._build(self)
159 app = out
160 self.store["app"] = app
--> 161 plotter = self._plotter_class(**self.store)
162 plotter.background_color = self.background_color
163 self._plotter = plotter
TypeError: Plotter.__init__() got an unexpected keyword argument 'multi_samples'
Here’s my specs:
- MNE version: 1.6.0
- operating system: CentOS 7.6.1810
Before running the code, I load the modules python/python3.6 and freesurfer/6.0.0.
Do you know where the problem can come from?
Thanks in advance 
I’ll leave it opened if anybody gets an idea.