I am having issues with the gui function and show_view, following the ecog tutorial in MNE’s webpage.
First of all, MNE and OS versions are:
- MNE version: e.g. 0.24.1 - operating system: Ubuntu 24
The functions are:
mne.gui.locate_ieeg
show_view
The issue is not regarding errors caught, but that for both functions, the window only displays for less than a second, where in the case of the GUI, the window displays but it is all black.
Does anyone have any idea why or had similar issues?
Hmmm sounds like an issue with mne.viz.Brain which is the 3D brain renderer that uses pyvista. Can you share the output of running mne sys_info in a terminal? This may also be solved by running pip install -U pyvista pyvistaqt.
place/lib/python3.9/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
warn("Fetchers from the nilearn.datasets module will be "
place/main.py:17: RuntimeWarning: Could not parse meas date from the header. Setting to None.
raw = mne.io.read_raw_cnt('ecog_place/FResende/sEEG_tasksMemoryEmotionsNPS18122015/sEEG_FR_almoco.cnt')
Using normal I/O
Creating tag directory for /place/python3.9/site-packages/mne/data/fsaverage/fsaverage-fiducials.fif...
start { 0
start { 107
block = 107 nent = 4 nchild = 0
end } 107
block = 0 nent = 4 nchild = 1
end } 0
[done]
Reading FreeSurfer talairach.xfm file:
/ecog_place/FResende/MRI_CT/fsaverage/subject/mri/transforms/talairach.xfm
Found: 'MNI Transform File'
Loading /ecog_place/FResende/MRI_CT/fsaverage/subject/mri/brain.mgz
Using pyvistaqt 3d backend.
THE END MY FRIEND
Traceback (most recent call last):
File "/place/main.py", line 29, in <module>
exit()
File "/place/python3.9/_sitebuiltins.py", line 26, in __call__
raise SystemExit(code)
SystemExit: None
(2)Check the soft link " libstdc++.so.6" and the target file"libstdc++.so.6.0.30" (My system has libstdc++.so.6.0.30 in that folder, yours may be libstdc++.so.6.0.29 or 28)is the same (name and size) in both paths “/lib/x86_64-linux-gnu” and " /path to your anaconda/anaconda3/lib"
cd /lib/x86_64-linux-gnu
ls -al | grep libstdc++
cd /home/xxx/anaconda3/lib (I installed the anaconda here)
ls -al | grep libstdc++
If the above files are not the same in both paths:
(a)Delete the soft link “libstdc++.so, libstdc++.so.6” and target file “libstdc++.so.6.0.X” in the path “/home/xxx/anaconda3/lib”
(b)copy the target file “libstdc++.so.6.0.X” from “/lib/x86_64-linux-gnu” to " /home/xxx/anaconda3/lib":