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

FAIRS Amie amie.FAIRS at univ-amu.fr
Fri Jul 3 07:33:16 EDT 2020
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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?



Dr. Amie Fairs
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<mailto: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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