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

[Dan McCloy]

        External Email - Use Caution        

I'm not sure but I think pyvista 0.25.3 is only compatible with latest development version of MNE-python? You could try downgrading:
pip install pyvista=0.24

-- dan
Daniel McCloy
https://dan.mccloy.info
Research Scientist
Institute for Learning and Brain Sciences
University of Washington

-------- Original Message --------
On Jul 3, 2020, 06:02, Luke Bloy wrote:

> 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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