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<body lang="EN-GB" link="#0563C1" vlink="#954F72"><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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<p class="MsoNormal"><span lang="FR">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR"><o:p> </o:p></span></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m using spyder from within anaconda, and my sys_info is:<o:p></o:p></p>
<p class="MsoNormal">mne sys_info<o:p></o:p></p>
<p class="MsoNormal">Platform: Linux-5.3.0-61-generic-x86_64-with-debian-buster-sid<o:p></o:p></p>
<p class="MsoNormal">Python: 3.7.6 (default, Jan 8 2020, 19:59:22) [GCC 7.3.0]<o:p></o:p></p>
<p class="MsoNormal">Executable: /home/developer/anaconda3/bin/python<o:p></o:p></p>
<p class="MsoNormal">CPU: x86_64: 6 cores<o:p></o:p></p>
<p class="MsoNormal">Memory: 19.8 GB<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">mne: 0.20.7<o:p></o:p></p>
<p class="MsoNormal">numpy: 1.18.1 {blas=mkl_rt, lapack=mkl_rt}<o:p></o:p></p>
<p class="MsoNormal">scipy: 1.4.1<o:p></o:p></p>
<p class="MsoNormal">matplotlib: 3.1.3 {backend=Qt5Agg}<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">sklearn: 0.22.1<o:p></o:p></p>
<p class="MsoNormal">numba: 0.48.0<o:p></o:p></p>
<p class="MsoNormal">nibabel: 3.1.1<o:p></o:p></p>
<p class="MsoNormal">cupy: Not found<o:p></o:p></p>
<p class="MsoNormal">pandas: 1.0.1<o:p></o:p></p>
<p class="MsoNormal">dipy: 1.1.1<o:p></o:p></p>
<p class="MsoNormal">mayavi: 4.7.2.dev0 {qt_api=pyqt5, PyQt5=5.10}<o:p></o:p></p>
<p class="MsoNormal">pyvista: 0.25.3<o:p></o:p></p>
<p class="MsoNormal">vtk: 9.0.1<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I type mne coreg into the command line I get:<o:p></o:p></p>
<p class="MsoNormal">mne coreg<o:p></o:p></p>
<p class="MsoNormal">Stack dump:<o:p></o:p></p>
<p class="MsoNormal">Fatal Python error: Segmentation fault<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thread 0x00007fc9da677700 (most recent call first):<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/threading.py", line 296 in wait<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/queue.py", line 170 in get<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/mne/gui/_coreg_gui.py", line 1368 in worker<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/threading.py", line 870 in run<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/threading.py", line 926 in _bootstrap_inner<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/threading.py", line 890 in _bootstrap<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Current thread 0x00007fca60f2d740 (most recent call first):<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/tvtk/pyface/ui/qt4/QVTKRenderWindowInteractor.py", line 370 in paintEvent<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/tvtk/pyface/ui/qt4/scene.py", line 69 in paintEvent<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/pyface/util/guisupport.py", line 137 in start_event_loop_qt4<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/traitsui/qt4/view_application.py", line 132 in __init__<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/traitsui/qt4/view_application.py", line 85 in view_application<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/traitsui/qt4/toolkit.py", line 224 in view_application<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/traits/has_traits.py", line 2351 in configure_traits<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/mne/gui/__init__.py", line 18 in _initialize_gui<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/mne/gui/__init__.py", line 180 in coregistration<o:p></o:p></p>
<p class="MsoNormal"> File "<decorator-gen-421>", line 21 in coregistration<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/mne/commands/mne_coreg.py", line 118 in run<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/lib/python3.7/site-packages/mne/commands/utils.py", line 107 in main<o:p></o:p></p>
<p class="MsoNormal"> File "/home/developer/anaconda3/bin/mne", line 8 in <module><o:p></o:p></p>
<p class="MsoNormal">Segmentation fault (core dumped)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Am I doing something entirely stupid? Does anyone know why this might not work and how I can make it work?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB">Amie<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB">------------------
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB">Dr. Amie Fairs<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB">Post-doctorant<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB">Aix-Marseille Université<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="mso-fareast-language:EN-GB">Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Email : </span><span lang="FR" style="mso-fareast-language:EN-GB"><a href="mailto:amie.fairs@univ-amu.fr"><span lang="EN-GB">amie.fairs@univ-amu.fr</span></a></span><span style="mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours.<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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