[Mne_analysis] mne.gui.coregistration crashing, maybe a mayavi issue

[Luke Bloy]

        External Email - Use Caution        

Have you tried with

export MESA_GL_VERSION_OVERRIDE=3.3
export MNE_3D_OPTION_ANTIALIAS=false

before launching mne?

On my virtual linux machines this lets me get some visualization,
although I still have some issues with seeing the fiducial points,
depending on opacity levels.

Luke


On Fri, Jul 3, 2020 at 7:33 AM FAIRS Amie <amie.FAIRS at univ-amu.fr> wrote:

>         External Email - Use Caution
>
> Dear all,
>
>
>
> I’m using mne python for source reconstruction and need to align my
> coordinate frames, using mne.gui.coregistration. However, it is crashing
> and I don’t know how to fix it. The GUI box briefly flashes, disappears,
> and then my kernel restarts.
>
>
>
> I’m using spyder from within anaconda, and my sys_info is:
>
> mne sys_info
>
> Platform:      Linux-5.3.0-61-generic-x86_64-with-debian-buster-sid
>
> Python:        3.7.6 (default, Jan  8 2020, 19:59:22)  [GCC 7.3.0]
>
> Executable:    /home/developer/anaconda3/bin/python
>
> CPU:           x86_64: 6 cores
>
> Memory:        19.8 GB
>
>
>
> mne:           0.20.7
>
> numpy:         1.18.1 {blas=mkl_rt, lapack=mkl_rt}
>
> scipy:         1.4.1
>
> matplotlib:    3.1.3 {backend=Qt5Agg}
>
>
>
> sklearn:       0.22.1
>
> numba:         0.48.0
>
> nibabel:       3.1.1
>
> cupy:          Not found
>
> pandas:        1.0.1
>
> dipy:          1.1.1
>
> mayavi:        4.7.2.dev0 {qt_api=pyqt5, PyQt5=5.10}
>
> pyvista:       0.25.3
>
> vtk:           9.0.1
>
>
>
> The linux platform is running through a virtual machine on my windows
> computer – I need to do it this way because some of the mne commands need
> freesurfer and that is in linux. In case it is relevant: before crashing,
> memory usage is around 16GB (almost 20 GB are assigned to the virtual
> machine, out of 32GB total).
>
>
>
> If I type mne coreg into the command line I get:
>
> mne coreg
>
> Stack dump:
>
> Fatal Python error: Segmentation fault
>
>
>
> Thread 0x00007fc9da677700 (most recent call first):
>
>   File "/home/developer/anaconda3/lib/python3.7/threading.py", line 296 in
> wait
>
>   File "/home/developer/anaconda3/lib/python3.7/queue.py", line 170 in get
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/mne/gui/_coreg_gui.py",
> line 1368 in worker
>
>   File "/home/developer/anaconda3/lib/python3.7/threading.py", line 870 in
> run
>
>   File "/home/developer/anaconda3/lib/python3.7/threading.py", line 926 in
> _bootstrap_inner
>
>   File "/home/developer/anaconda3/lib/python3.7/threading.py", line 890 in
> _bootstrap
>
>
>
> Current thread 0x00007fca60f2d740 (most recent call first):
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/tvtk/pyface/ui/qt4/QVTKRenderWindowInteractor.py",
> line 370 in paintEvent
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/tvtk/pyface/ui/qt4/scene.py",
> line 69 in paintEvent
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/pyface/util/guisupport.py",
> line 137 in start_event_loop_qt4
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/traitsui/qt4/view_application.py",
> line 132 in __init__
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/traitsui/qt4/view_application.py",
> line 85 in view_application
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/traitsui/qt4/toolkit.py",
> line 224 in view_application
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/traits/has_traits.py",
> line 2351 in configure_traits
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/mne/gui/__init__.py",
> line 18 in _initialize_gui
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/mne/gui/__init__.py",
> line 180 in coregistration
>
>   File "<decorator-gen-421>", line 21 in coregistration
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/mne/commands/mne_coreg.py",
> line 118 in run
>
>   File
> "/home/developer/anaconda3/lib/python3.7/site-packages/mne/commands/utils.py",
> line 107 in main
>
>   File "/home/developer/anaconda3/bin/mne", line 8 in <module>
>
> Segmentation fault (core dumped)
>
>
>
>
>
> I think this could be a mayavi issue because I also cannot launch
> mne.viz.plot_alignment(), as a mayavi image object is created that remains
> blank, crashes the computer, and I have to restart. I saw in a git issue
> some other people had seg fault issues and one check was to test with
> mlab.test_plot3d(), which crashes the kernel and then brings up warnings
> when the kernel restarts itself.
>
>
>
> Am I doing something entirely stupid? Does anyone know why this might not
> work and how I can make it work?
>
>
>
> Best,
>
>
>
> Amie
>
>
>
> ------------------
>
> Dr. Amie Fairs
>
> Post-doctorant
>
> Aix-Marseille Université
>
> Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur |
> 13100 Aix-en-Provence
>
> Email : amie.fairs at univ-amu.fr
>
>
>
> While I may send this email outside of typical working hours, I have no
> expectation to receive an email outside of your typical hours.
>
>
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