MNE version: 0.24.0 operating system: Linux on Docker I’m trying to run the MRI reconstruction example without success on a headless installation on Docker The best attempt following other discussion about 3d visualization and the use of pyvista seems to be the following: import os import mne f…

I’d suggest that you take a look at GitHub - mne-tools/mne-docker: Repository for mne docker images as a starting place for docker and singularity images. And also a place to incorporate any improvements that you might come up with. To solve the blank screen issue, I’d try setting this env variable …

Does mne sys_info tell you that you have 3D capabilities? If it segfaults, you do not :slight_smile: Have you seen Advanced setup — MNE 0.24.1 documentation ?

@larsoner thanks for your reply. This is the output Matplotlib is building the font cache; this may take a moment. qt.qpa.xcb: could not connect to display qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt pla…

Hmm, so it is trying to use the PyQt5 backend. This is actually a general PyQt5 issue. See the reply about QT_DEBUG_PLUGINS here: [locomotion] “Failed to load platform plugin ”xcb“ ” while launching qt5 app on linux without qt installed plugins, qt, qt5 asked by …

Yes my goal is to make the brain visualization work on a notebook (see code above). I can get the notebook backend with pyvista backend work (with the panel backend for instance), but I get a black screen on mne with the brain viz. For instance, this works: from pyvista import demos from pyvista.…

This is my Docker image definition: FROM jupyter/base-notebook:hub-1.4.2 USER root # install utils RUN apt-get -y update RUN apt-get -y install software-properties-common RUN add-apt-repository "deb http://us.archive.ubuntu.com/ubuntu bionic main universe" RUN apt-get -y update RUN apt-get -y inst…

After your set_3d_backend call, if you do get_3d_backend() does it say 'notebook'? Maybe you are missing some dependency. For what it’s worth, this is the conda env we use in CI testing for the notebook: mne-tools/mne-python/blob/main/server_environment.yml name: base channels: - c…

I think @bloyl made an awesome job in GitHub - bloyl/mne_docker and although it’s marked as work in progress, it might be enough for your needs? I think it’s worth looking at

@larsoner I will try that environment file, thanks. What I see a black figure with the required libraries installed [image] Installed packages: Package Version Editable project location ----------------------------- ---------- ---------------------------------- aiohttp …

I have had the same difficulty trying to use Ubuntu 20.04 in WSL. With ipyvtklink, I can get pyvista code to work but mne just displays a black image. I then tried using Ubuntu 20.04 in VirtualBox and got the same black image running code directly. I created an environment as follows wget https:/…

Thanks. That fixes both for me. Is there some way to add this to the linux installation instructions?

Support for 3D brain visualization in headless mode?

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richard (Richard Höchenberger) Split this topic May 20, 2022, 10:37pm 15

A post was split to a new topic: Using MNE with 3D visualization on a headless server

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Support for 3D brain visualization in headless mode?

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