# Segmentation fault when visualizing the brain **URL:** \ **Category:** Support & Discussions\ **Tags:** installation\ **Created:** [February 11, 2025, 12:36pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785 "2025-02-11T12:36:55Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![okapi](https://avatars.discourse-cdn.com/v4/letter/o/da6949/32.png) [@okapi](https://mne.discourse.group/u/okapi)\ **Post date:** [February 11, 2025, 12:36pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/1 "2025-02-11T12:36:55Z")
- MNE version: 1.9.0 (using MNE-Python installers) - operating system: e.g. macOS 12 / Windows 10 / Ubuntu 18.04 Dear MNE experts, I have a problem when trying to visualize 3D brains on local computer for all kinds of 3d brain visualizations I tried involving pyvista. To install MNE, I use MNE-Python installers. As an example, I have the error when running this code example with data provided: [https://mne.tools/1.8/auto\_examples/visualization/parcellation.html#sphx-glr-auto-examples-visualization-parcellation-py](https://mne.tools/1.8/auto_examples/visualization/parcellation.html#sphx-glr-auto-examples-visualization-parcellation-py) Error occurs in this line: [brain](https://mne.tools/1.8/generated/mne.viz.Brain.html#mne.viz.Brain) = [Brain](https://mne.tools/1.8/generated/mne.viz.Brain.html#mne.viz.Brain)( “fsaverage”, “lh”, “inflated”, [subjects\_dir](https://docs.python.org/3/library/pathlib.html#pathlib.PosixPath)=[subjects\_dir](https://docs.python.org/3/library/pathlib.html#pathlib.PosixPath), cortex=“low\_contrast”, background=“white”, size=(800, 600), ) The error: Using pyvistaqt 3d backend. /usr/lib/python3/dist-packages/spyder/plugins/ipythonconsole/scripts/ conda-activate.sh: line 18: 9782 Segmentation fault (core dumped) $CONDA\_ENV\_PYTHON -m spyder\_kernels.console -f $SPYDER\_KERNEL\_SPEC Fatal Python error: Segmentation fault Main thread: Current thread 0x00007d484ca4e600 (most recent call first): File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ pyvista/plotting/render\_window\_interactor.py”, line 1372 in initialize File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ pyvistaqt/plotting.py”, line 287 in \_setup\_interactor File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ pyvistaqt/plotting.py”, line 247 in **init** File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ pyvistaqt/plotting.py”, line 572 in **init** File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ viz/backends/\_pyvista.py”, line 150 in \_build File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ viz/backends/\_pyvista.py”, line 256 in **init** File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ viz/backends/\_qt.py”, line 1777 in **init** File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ viz/backends/\_utils.py”, line 391 in func File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ viz/backends/renderer.py”, line 53 in \_get\_renderer File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ gui/\_coreg.py”, line 284 in **init** File “”, line 12 in **init** File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ viz/backends/\_utils.py”, line 391 in func File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/mne/ gui/\_gui.py”, line 149 in coregistration File “”, line 12 in coregistration File “/home/okapi/.config/spyder-py3/temp.py”, line 21 in File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ spyder\_kernels/py3compat.py”, line 356 in compat\_exec File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ spyder\_kernels/customize/spydercustomize.py”, line 473 in exec\_code File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ spyder\_kernels/customize/spydercustomize.py”, line 740 in \_exec\_cell File “/home/okapi/mne-python/1.9.0\_0/lib/python3.12/site-packages/ spyder\_kernels/customize/spydercustomize.py”, line 689 in runcell File “/tmp/ipykernel\_9782/1346111906.py”, line 1 in Which results in restartig the kernel. At first, I suspected the issue might be related to my GPU. However, basic 3D visualization seems to work. For example, I tried to display a sphere using pyvista: import pyvista as pv mesh = pv.Sphere() p = pv.Plotter() p.add\_mesh(mesh) mesh.plot() p.show() The sphere renders correctly, and I can interact with it. As I faced the same error for previous MNE versions too, I suppose it’s not just version-related issue. I would be very grateful for any help or suggestions! All the best, Viktoria ---
**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\ **Post date:** [February 15, 2025, 9:53am UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/2 "2025-02-15T09:53:28Z")
Hello, which operating system is that? Best wishes, Richard ---
**Author:** ![okapi](https://avatars.discourse-cdn.com/v4/letter/o/da6949/32.png) [@okapi](https://mne.discourse.group/u/okapi)\ **Post date:** [February 15, 2025, 10:09am UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/3 "2025-02-15T10:09:11Z")
Hello, Sorry, I must have removed this info by mistake during editing… I have Linux, Ubuntu 24.04.2 LTS ---
**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\ **Post date:** [February 15, 2025, 10:59am UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/4 "2025-02-15T10:59:26Z")
@larsoner Would you have time to look into this? ---
**Author:** ![okapi](https://avatars.discourse-cdn.com/v4/letter/o/da6949/32.png) [@okapi](https://mne.discourse.group/u/okapi)\ **Post date:** [February 15, 2025, 10:11pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/5 "2025-02-15T22:11:00Z")
I think that it’s a problem of 1.9.0 version of MNE, or its installer: I returned back to version 1.7.0 (also Installer) and the error disappeared. Also, in 1.9.0 version I had a problem when trying to plot raw file, just raw.plot(): in Spyder I had this error, no interactive window opened: “Using qt as 2D backend. ERROR:root:Cannot activate multiple GUI eventloops”, and in MNE console I had an error when closing interactive window: “RuntimeWarning: Failed to disconnect (None) from signal “triggered()”.” ---
**Author:** ![larsoner](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/larsoner/32/3_2.png) [@larsoner](https://mne.discourse.group/u/larsoner)\ **Post date:** [February 18, 2025, 3:54pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/6 "2025-02-18T15:54:08Z")
Can you run `mne sys_info` or `>>> import mne; mne.sys_info()` ? It should tell us info about your GPU etc. It’s possible it’s not new enough for 3D viz using newer VTK ---
**Author:** ![okapi](https://avatars.discourse-cdn.com/v4/letter/o/da6949/32.png) [@okapi](https://mne.discourse.group/u/okapi)\ **Post date:** [February 18, 2025, 4:22pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/7 "2025-02-18T16:22:03Z")
> [@larsoner](#): > > import mne; mne.sys\_info() Sure, thanks! Platform Linux-6.11.0-17-generic-x86\_64-with-glibc2.39 Python 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:50:58) [GCC 12.3.0] Executable /home/okapi/mne-python/1.7.1\_0/bin/python CPU x86\_64 (16 cores) Memory 15.0 GB Core ├☒ mne 1.7.1 (outdated, release 1.9.0 is available!) ├☑ numpy 1.26.4 (OpenBLAS 0.3.27 with 16 threads) ├☑ scipy 1.13.1 └☑ matplotlib 3.8.4 (backend=Qt5Agg) Numerical (optional) ├☑ sklearn 1.5.0 ├☑ numba 0.59.1 ├☑ nibabel 5.2.1 ├☑ nilearn 0.10.4 ├☑ dipy 1.9.0 ├☑ openmeeg 2.5.11 ├☑ pandas 2.2.2 ├☑ h5io 0.2.3 ├☑ h5py 3.11.0 └☐ unavailable cupy Visualization (optional) ├☑ pyvista 0.43.9 (OpenGL 4.6 (Core Profile) Mesa 24.2.8-1ubuntu1~24.04.1 via AMD Radeon Graphics (radeonsi, renoir, LLVM 19.1.1, DRM 3.59, 6.11.0-17-generic)) ├☑ pyvistaqt 0.11.0 ├☑ vtk 9.2.6 ├☑ qtpy 2.4.1 (PyQt5=5.15.8) ├☑ ipympl 0.9.4 ├☑ pyqtgraph 0.13.7 ├☑ mne-qt-browser 0.6.3 ├☑ ipywidgets 8.1.3 ├☑ trame\_client 3.1.0 ├☑ trame\_server 3.0.1 ├☑ trame\_vtk 2.8.9 └☑ trame\_vuetify 2.6.0 Ecosystem (optional) ├☑ mne-bids 0.15.0 ├☑ mne-nirs 0.6.0 ├☑ mne-features 0.3 ├☑ mne-connectivity 0.7.0 ├☑ mne-icalabel 0.6.0 ├☑ mne-bids-pipeline 1.8.0 ├☑ neo 0.13.0 ├☑ eeglabio 0.0.2-4 ├☑ edfio 0.4.2 ├☑ mffpy 0.9.0 └☑ pybv 0.7.5 ---
**Author:** ![larsoner](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/larsoner/32/3_2.png) [@larsoner](https://mne.discourse.group/u/larsoner)\ **Post date:** [February 18, 2025, 4:33pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/8 "2025-02-18T16:33:13Z")
That must be for the old/working install, can you give the one for the new/broken 1.9 one? ---
**Author:** ![okapi](https://avatars.discourse-cdn.com/v4/letter/o/da6949/32.png) [@okapi](https://mne.discourse.group/u/okapi)\ **Post date:** [March 3, 2025, 5:45pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/9 "2025-03-03T17:45:27Z")
Hello, Sorry I was able to uninstall old version and install new one only now. Here’s the output for 1.9 version: Platform Linux-6.11.0-17-generic-x86\_64-with-glibc2.39 Python 3.12.7 | packaged by conda-forge | (main, Oct 4 2024, 16:05:46) [GCC 13.3.0] Executable /home/okapi/mne-python/1.9.0\_0/bin/python CPU AMD Ryzen 7 5700U with Radeon Graphics (16 cores) Memory 15.0 GiB Core ├☑ mne 1.9.0 (latest release) ├☑ numpy 1.26.4 (OpenBLAS 0.3.28 with 16 threads) ├☑ scipy 1.14.1 └☑ matplotlib 3.10.0 (backend=module://matplotlib\_inline.backend\_inline) Numerical (optional) ├☑ sklearn 1.6.0 ├☑ numba 0.60.0 ├☑ nibabel 5.3.2 ├☑ nilearn 0.11.0 ├☑ dipy 1.10.0 ├☑ openmeeg 2.5.14 ├☑ pandas 2.2.3 ├☑ h5io 0.2.4 ├☑ h5py 3.12.1 └☐ unavailable cupy Visualization (optional) ├☑ pyvista 0.44.2 (OpenGL 4.6 (Core Profile) Mesa 24.2.8-1ubuntu1~24.04.1 via AMD Radeon Graphics (radeonsi, renoir, LLVM 19.1.1, DRM 3.59, 6.11.0-17-generic)) ├☑ pyvistaqt 0.11.1 ├☑ vtk 9.3.1 ├☑ qtpy 2.4.2 (PySide6=6.7.3) ├☑ ipympl 0.9.5 ├☑ pyqtgraph 0.13.7 ├☑ mne-qt-browser 0.6.3 ├☑ ipywidgets 8.1.5 ├☑ trame\_client 3.5.0 ├☑ trame\_server 3.2.3 ├☑ trame\_vtk 2.8.12 └☑ trame\_vuetify 2.7.2 Ecosystem (optional) ├☑ mne-bids 0.16.0 ├☑ mne-nirs 0.7.1 ├☑ mne-features 0.3 ├☑ mne-connectivity 0.7.0 ├☑ mne-icalabel 0.7.0 ├☑ mne-bids-pipeline 1.9.0 ├☑ neo 0.13.4 ├☑ eeglabio 0.0.3 ├☑ edfio 0.4.5 ├☑ mffpy 0.10.0 └☑ pybv 0.7.6 ---
**Author:** ![larsoner](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/larsoner/32/3_2.png) [@larsoner](https://mne.discourse.group/u/larsoner)\ **Post date:** [March 5, 2025, 4:22pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/10 "2025-03-05T16:22:00Z")
Plain PyVista working does suggest it’s not a 3D issue most likely. But plain PyVista doesn’t use Qt, and `Brain` does, so it’s probably a Qt issue. Does it work if you run your code from a plain `python` console as opposed to running it from Spyder (which it looks like you’re doing)? I wonder if you maybe don’t have Spyder configured properly to use the MNE-Python env correctly somehow ---
**Author:** ![okapi](https://avatars.discourse-cdn.com/v4/letter/o/da6949/32.png) [@okapi](https://mne.discourse.group/u/okapi)\ **Post date:** [March 5, 2025, 9:45pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/11 "2025-03-05T21:45:10Z")
> [@okapi](#): > > Also, in 1.9.0 version I had a problem when trying to plot raw file, just raw.plot(): in Spyder I had this error, no interactive window opened: “Using qt as 2D backend. ERROR:root:Cannot activate multiple GUI eventloops”, and in MNE console I had an error when closing interactive window: “RuntimeWarning: Failed to disconnect (None) from signal “triggered()”.” No, it doesn’t work in console too, and more than that, I could not plot raw file either, so it was not just a problem of 3d brain somehow… I wrote about it in the comment above: "Also, in 1.9.0 version I had a problem when trying to plot raw file, just raw.plot(): in Spyder I had this error, no interactive window opened: “Using qt as 2D backend. ERROR:root:Cannot activate multiple GUI eventloops”, and in MNE console I had an error when closing interactive window: “RuntimeWarning: Failed to disconnect (None) from signal “triggered()”.” I don’t understand what can cause such a massive error… ---
**Author:** ![larsoner](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/larsoner/32/3_2.png) [@larsoner](https://mne.discourse.group/u/larsoner)\ **Post date:** [March 6, 2025, 7:08pm UTC](https://mne.discourse.group/t/segmentation-fault-when-visualizing-the-brain/10785/12 "2025-03-06T19:08:06Z")
2D plotting with the mne-qt-browser backend at least uses OpenGL. But both mne-qt-browser and the matplotlib backend will probably depend on having a Qt backend available. So I wonder if your Qt implementation is somehow broken. Another possibility is that it’s a `wayland` issue – if you `echo $XDG_SESSION_DESKTOP` is it xorg or wayland?