I experience problems with 3d plotting. I used to use mayavi, but since it has been discontinued only matplotlib works for me (which looks a bit ugly). pyvistaqt 3d backend returns an empty plot.
MNE version 1.1.1
System
NAME=“Debian GNU/Linux”
VERSION_ID=“11”
VERSION=“11 (bullseye)”
VERSION_CODENAME=bullseye
ID=debian
I am trying to plot source estimate with a simple line stc.plot(subject). The subject is ‘fsaverage’.
The output looks like that (below). When I press play, nothing is showing on the top plot, but the bottom plot is changing.
if that doesn’t work, please share the result of mne.sys_info()
If it does work with sample data but not with your data, please share a complete code sample, so we can hopefully see what might be going wrong. (It’s hard to tell if all we know is “I tried stc.plot('fsaverage') and it didn’t work”.) If possible include a link to the data file (if it’s huge, a cropped version of just 1-2 seconds is fine), so we can try to fully reproduce.
Thank you for your suggestions! I apologize for the insufficient description.
I downloaded sample data and followed this tutorial for plotting Plotting with mne.viz.Brain — MNE 1.2.dev0 documentation. Unfortunately, the result is the same.
The output
mne.sys_info()
Platform: Linux-5.10.0-17-amd64-x86_64-with-glibc2.31
Python: 3.9.2 (default, Feb 28 2021, 17:03:44) [GCC 10.2.1 20210110]
Executable: /data/u_studenova_software/PycharmProjects/source-space-connectivity-optimization/venv/bin/python
CPU: : 24 cores
Memory: 250.9 GB
mne: 1.1.1
numpy: 1.23.3 {}
scipy: 1.9.1
matplotlib: 3.6.0Backend QtAgg is interactive backend. Turning interactive mode on.
{backend=QtAgg}
sklearn: 1.1.2
numba: 0.56.2
nibabel: 4.0.2
nilearn: 0.9.2
dipy: 1.5.0
cupy: Not found
pandas: 1.5.0
pyvista: 0.36.1 {OpenGL 4.5 (Core Profile) Mesa 20.3.5 via llvmpipe (LLVM 11.0.1, 256 bits)}
pyvistaqt: 0.9.0
ipyvtklink: Matplotlib support failed
Traceback (most recent call last):
File "/afs/cbs.mpg.de/software/pycharm/2022.2/debian-bullseye-amd64/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 25, in do_import
succeeded = activate_func()
File "/afs/cbs.mpg.de/software/pycharm/2022.2/debian-bullseye-amd64/plugins/python-ce/helpers/pydev/pydev_ipython/matplotlibtools.py", line 155, in activate_pylab
pylab = sys.modules['pylab']
KeyError: 'pylab'
0.2.3
vtk: 9.1.0
qtpy: 2.2.0 {PyQt5=5.15.2}
ipympl: 0.9.2
pyqtgraph: 0.13.1
pooch: v1.6.0
mne_bids: Not found
mne_nirs: Not found
mne_features: Not found
mne_qt_browser: 0.4.0
mne_connectivity: Not found
mne_icalabel: Not found
Before starting, I made a fresh environment with pip-installed-modules from environment.yml file. Shall I now install “not found” and pylab?
Hello @astudenova, please follow our official installation instructions (using conda or our standalone installers, notpip) to ensure you end up with a working installation. It’s tricky getting everything working right “by hand” and with pip alone.
Best wishes,
Richard
Edit I just now realized you’re relying on Notebook support for 3D rendering. I don’t think we have a similarly straightforward procedure as for the “non-Notebook” setup Sorry.
Thank you very much for suggestions!
I went through conda installations, but it did not solve the problem.
But mne.viz.set_3d_options(antialias=False) did! mne.sys_info() runs without errors, and I got my brain back! Thank you!
I was also trying to do stc.plot() with my linux system. However, I keep getting the error ‘Cannot connect to a valid display’. Is there another setting to configure for 3D visualization? Thank you in advance!
Sorry.