[Mne_analysis] Problem : transparent brain with plot_alignment.

Guillaume Favelier guillaume.favelier at inria.fr
Wed Jun 10 11:34:09 EDT 2020
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Hello Jacques, 

Do you mind sharing the full report? 

python -c "import mne; mne.sys_info()" 

We expect more information especially PyQt5, VTK and PyVista. 

Personally, I think that this kind of transparency issue is not unknown with mayavi 
and the origin can range from an incompatibility issue with intel integrated graphic 
cards, the gpu driver version or the behaviour of vtk around opacity in general. 

The easiest way i know to fix this for mayavi is to enable depth peeling: 


But this comes at the price of slightly heavier rendering operations. 

Another option is to change the 3d backend to pyvista before the plot: 


Hopefully this helps, 


> De: "Jacques Pesnot" <jacques.pesnot at hotmail.fr>
> À: "mne analysis" <mne_analysis at nmr.mgh.harvard.edu>
> Envoyé: Mercredi 10 Juin 2020 12:05:38
> Objet: [Mne_analysis] Problem : transparent brain with plot_alignment.

> External Email - Use Caution

> Hi MNE team !

> I have a problem with "mne.viz.plot_alignment". The function plots a transparent
> brain, and I don't manage to change the transparency level. The weird thing is
> that I don't reproduce the ECOG figure from the MNE website.
> --> I used the script available on the website here : [
> https://mne.tools/dev/auto_examples/visualization/plot_3d_to_2d.html#sphx-glr-auto-examples-visualization-plot-3d-to-2d-py
> |
> https://mne.tools/dev/auto_examples/visualization/plot_3d_to_2d.html#sphx-glr-auto-examples-visualization-plot-3d-to-2d-py
> ]
> --> This is what I get :

> For info :
> My system is Ubuntu 18.04.4 LTS
> MNE is 0.20.0
> mayavi is 4.7.1
> matplotlib is 3.1.3

> Thanks a lot !
> Jacques.

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