Segmentation fault when visualizing the brain

💬 Support & Discussions
1
  • 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

Error occurs in this line:

brain = Brain( “fsaverage”, “lh”, “inflated”, subjects_dir=subjects_dir, 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

2

Hello, which operating system is that?

Best wishes,
Richard

3

Hello,
Sorry, I must have removed this info by mistake during editing…
I have Linux, Ubuntu 24.04.2 LTS

1 Like
4

@larsoner Would you have time to look into this?

5

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()”.”

1 Like
6

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

7

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

8

That must be for the old/working install, can you give the one for the new/broken 1.9 one?

9

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

10

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

11

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…

12

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?