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<body dir="ltr"><p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p>
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Thanks a lot <span style="font-family: arial, helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">Guillaume for your (super quick !) answer ! </span></div>
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<span style="font-family: arial, helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">I tried what you have suggested but did not manage to solve the problem ... So I spent the last 4 hours -_-' trying different things and
found that the problem was coming from Ubuntu driver. So for the record, I installed the NVIDIA driver and disabled the "nouveau" default driver as indicated here : <a href="https://linuxconfig.org/how-to-install-the-nvidia-drivers-on-ubuntu-18-04-bionic-beaver-linux">https://linuxconfig.org/how-to-install-the-nvidia-drivers-on-ubuntu-18-04-bionic-beaver-linux</a></span></div>
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<img size="195875" contenttype="image/png" unselectable="on" tabindex="-1" style="user-select: none; width: 198.549px; height: 186.4px;" data-imgsize="custom" width="198.54934823091247" height="186.40034965034965" data-outlook-trace="F:1|T:1" src="cid:f394ffe9-abb9-493e-b5f0-8310bf7035f4"><br>
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For info, my "<span style="font-family: arial, helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">mne.sys_info()" was :</span></div>
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<pre style="box-sizing: border-box; overflow: auto; font-family: monospace; font-size: 14px; display: block; padding: 1px 0px; margin: 0px; word-break: break-all; overflow-wrap: break-word; background-color: rgb(255, 255, 255); border-radius: 0px; text-align: left">Platform: Linux-5.3.0-53-generic-x86_64-with-debian-buster-sid
Python: 3.7.6 (default, Jan 8 2020, 19:59:22) [GCC 7.3.0]
Executable: /home/jacques/anaconda3/bin/python
CPU: x86_64: 16 cores
Memory: 31.3 GB
mne: 0.20.0
numpy: 1.18.5 {blas=openblas, lapack=openblas}
scipy: 1.4.1
matplotlib: 3.1.3 {backend=module://ipykernel.pylab.backend_inline}
sklearn: 0.22.1
numba: 0.48.0
nibabel: 3.1.0
cupy: Not found
pandas: 1.0.1
dipy: Not found
mayavi: 4.7.1 {qt_api=pyqt5, PyQt5=5.15.0}
pyvista: 0.25.3
vtk: 8.1.2</pre>
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<span style="font-family: arial, helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important"><span>Have a nice weekend ! </span></span></div>
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<span style="font-family: arial, helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important"><span>Jacques. </span></span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> de la part de Guillaume Favelier <guillaume.favelier@inria.fr><br>
<b>Envoyé :</b> mercredi 10 juin 2020 17:34<br>
<b>À :</b> mne analysis <mne_analysis@nmr.mgh.harvard.edu><br>
<b>Objet :</b> Re: [Mne_analysis] Problem : transparent brain with plot_alignment.</font>
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<p><span style="padding:3px 10px; border-radius:5px; color:#ffffff; font-weight:bold; display:inline-block; background-color:#ff0000"> External Email - Use Caution </span></p>
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<div>Hello Jacques,<br>
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<div>Do you mind sharing the full report?<br>
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<div>python -c "import mne; mne.sys_info()"<br>
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<div>We expect more information especially PyQt5, VTK and PyVista.<br>
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<div>Personally, I think that this kind of transparency issue is not unknown with mayavi</div>
<div>and the origin can range from an incompatibility issue with intel integrated graphic</div>
<div>cards, the gpu driver version or the behaviour of vtk around opacity in general.<br>
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<div>The easiest way i know to fix this for mayavi is to enable depth peeling:<br>
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<div>https://github.com/enthought/mayavi/issues/574<br>
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<div>But this comes at the price of slightly heavier rendering operations.<br>
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<div>Another option is to change the 3d backend to pyvista before the plot:<br>
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<div>mne.viz.set_3d_backend("pyvista")<br>
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<div>Hopefully this helps,<br>
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<div>Guillaume<br>
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<b>De: </b>"Jacques Pesnot" <jacques.pesnot@hotmail.fr><br>
<b>À: </b>"mne analysis" <mne_analysis@nmr.mgh.harvard.edu><br>
<b>Envoyé: </b>Mercredi 10 Juin 2020 12:05:38<br>
<b>Objet: </b>[Mne_analysis] Problem : transparent brain with plot_alignment.<br>
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<p><span style="padding:3px 10px; border-radius:5px; color:#ffffff; font-weight:bold; display:inline-block; background-color:#ff0000"> External Email - Use Caution </span></p>
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Hi MNE team !</div>
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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. </div>
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<span style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif; font-size:12pt">--> I used the script available on the website here : </span><a href="https://mne.tools/dev/auto_examples/visualization/plot_3d_to_2d.html#sphx-glr-auto-examples-visualization-plot-3d-to-2d-py" id="LPlnk443970" target="_blank" style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">https://mne.tools/dev/auto_examples/visualization/plot_3d_to_2d.html#sphx-glr-auto-examples-visualization-plot-3d-to-2d-py</a><br>
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--> This is what I get : </div>
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For info :</div>
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My system is Ubuntu 18.04.4 LTS</div>
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MNE is 0.20.0</div>
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mayavi is 4.7.1</div>
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matplotlib is 3.1.3</div>
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Thanks a lot !</div>
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Jacques. </div>
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