Mouse Offset in Brain Plot about mne-python

[welcome]

Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴

[larsoner]

What is your mne sys_info? It's possible this is a bug with PyQt5 and HiDPI (though it's more common on macOS than Linux)

[gedwald]

Thank you for the query; these are my two environments:

::: MacOS :::

Platform macOS-14.4.1-arm64-arm-64bit
Python 3.9.6 (default, Feb 3 2024, 15:58:27) [Clang 15.0.0 (clang-1500.3.9.4)]
Executable /Users/edwald/python_venvs/mne/bin/python3
CPU arm (8 cores)
Memory 16.0 GB

Core
├☑ mne 1.6.1 (latest release)
├☑ numpy 1.26.4 (OpenBLAS 0.3.23.dev with 8 threads)
├☑ scipy 1.12.0
├☑ matplotlib 3.8.3 (backend=module://matplotlib_inline.backend_inline)
├☑ pooch 1.8.0
└☑ jinja2 3.1.3

Numerical (optional)
├☑ sklearn 1.4.1.post1
├☑ nibabel 5.2.0
├☑ nilearn 0.10.3
├☑ pandas 2.2.0
└☐ unavailable numba, dipy, openmeeg, cupy

Visualization (optional)
├☑ pyvista 0.43.3 (OpenGL 4.1 Metal - 88 via Apple M1)
├☑ pyvistaqt 0.11.0
├☑ vtk 9.3.0
├☑ qtpy 2.4.1 (PyQt6=6.6.1)
├☑ pyqtgraph 0.13.4
├☑ mne-qt-browser 0.6.2
├☑ ipywidgets 8.1.2
└☐ unavailable ipympl, trame_client, trame_server, trame_vtk, trame_vuetify

Ecosystem (optional)
└☐ unavailable mne-bids, mne-nirs, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline

::: Ubuntu 22.04 :::

mne.sys_info()
Platform Linux-6.5.0-25-generic-x86_64-with-glibc2.35
Python 3.11.0rc1 (main, Aug 12 2022, 10:02:14) [GCC 11.2.0]
Executable /home/edwaldt20ni/VirtualEnvs/neweeg/bin/python
CPU x86_64 (12 cores)
Memory 62.6 GB

Core
├☑ mne 1.6.1 (latest release)
├☑ numpy 1.26.4 (OpenBLAS 0.3.23.dev with 12 threads)
├☑ scipy 1.12.0
├☑ matplotlib 3.8.3 (backend=QtAgg)
├☑ pooch 1.8.1
└☑ jinja2 3.1.3

Numerical (optional)
├☑ sklearn 1.4.1.post1
├☑ nibabel 5.2.0
├☑ nilearn 0.10.3
├☑ pandas 2.2.0
└☐ unavailable numba, dipy, openmeeg, cupy

Visualization (optional)
├☑ pyvista 0.43.3 (OpenGL 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 via llvmpipe (LLVM 15.0.7, 256 bits))
├☑ pyvistaqt 0.11.0
├☑ vtk 9.2.6
├☑ qtpy 2.4.1 (PyQt6=6.6.1)
├☑ pyqtgraph 0.13.3
├☑ mne-qt-browser 0.6.1
├☑ ipywidgets 8.1.2
└☐ unavailable ipympl, trame_client, trame_server, trame_vtk, trame_vuetify

Ecosystem (optional)
└☐ unavailable mne-bids, mne-nirs, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline

[larsoner]

If deemed helpful, I'll find a way to reduce the data and repeat the process with a smaller set of epochs

Can you try with this snippet (will download ~1.5GB):

import mne
data_path = mne.datasets.sample.data_path(verbose=True)
stc = mne.read_source_estimate(data_path / "MEG" / "sample" / "sample_audvis-meg-eeg-lh.stc", subject="sample")
stc.plot(subjects_dir=data_path / "subjects")

For me it produces something that interacts as expected, does it work for you?

[gedwald]

Not quite:
I haven’t had opportunity to test this on the Ubuntu box, but here’s what happens on the Mac.
I don’t know why it’s looking for an -fsaverage- file

(mne) edwald@temmi ~ % python
Python 3.9.6 (default, Feb 3 2024, 15:58:27)
[Clang 15.0.0 (clang-1500.3.9.4)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import mne
data_path=mne.datasets.sample.data_path(verbose=True)
Downloading file 'MNE-sample-data-processed.tar.gz' from 'https://osf.io/86qa2/download?version=6' to '/Users/edwald/mne_data'.
/Users/edwald/python_venvs/mne/lib/python3.9/site-packages/urllib3/init.py:35: NotOpenSSLWarning: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: urllib3/urllib3#3020
warnings.warn(
100%|█████████████████████████████████████| 1.65G/1.65G [00:00<00:00, 23.3TB/s]
Untarring contents of '/Users/edwald/mne_data/MNE-sample-data-processed.tar.gz' to '/Users/edwald/mne_data'
Download complete in 01m19s (1576.2 MB)
stc=mne.read_source_estimate(data_path / "MEG" / "sample" / "sample_audvis-meg-eeg-lh.stc", subject="sample")
stc.plot()
Traceback (most recent call last):
File "", line 1, in
File "/Users/edwald/python_venvs/mne/lib/python3.9/site-packages/mne/source_estimate.py", line 743, in plot
brain = plot_source_estimates(
File "", line 12, in plot_source_estimates
File "/Users/edwald/python_venvs/mne/lib/python3.9/site-packages/mne/viz/_3d.py", line 2398, in plot_source_estimates
subjects_dir = get_subjects_dir(subjects_dir=subjects_dir, raise_error=True)
File "/Users/edwald/python_venvs/mne/lib/python3.9/site-packages/mne/utils/config.py", line 475, in get_subjects_dir
subjects_dir = _check_fname(
File "", line 12, in _check_fname
File "/Users/edwald/python_venvs/mne/lib/python3.9/site-packages/mne/utils/check.py", line 263, in _check_fname
raise FileNotFoundError(f'{name} does not exist: "{fname}"')
FileNotFoundError: subjects_dir does not exist: "/Users/edwald/mne_data/MNE-fsaverage-data"
data_path
PosixPath('/Users/edwald/mne_data/MNE-sample-data')

[larsoner]

Argh sorry that last line in the MWE should be:

>>> stc.plot(subjects_dir=data_path / "subjects")

[gedwald]

Thank you -
the plot appears, but I can only get new dipole bubbles on the brain if I click the mouse on the extreme right edge
Ie. the V1 area and further up the edge. Then I get the bubbles on the lower edge of the brain. Any clicks further inwards on the brain do not visibly produce anything, probably because the bubble falls off the left edge of the brain plot. ( I have not rotated the plot at all).

[larsoner]

Okay I was able to replicate on my macOS machine -- can you see if being on this branch of PyVistaQt fixes things for you on mac at least?

pyvista/pyvistaqt#565

And maybe we'll get lucky and it'll also fix things on Linux.

[gedwald]

I’d happily do that, but I don’tknow how. Just clone a repository and build?best regardsT. EdwaldOn 22 Apr 2024, at 16:40, Eric Larson ***@***.***> wrote: Okay I was able to replicate on my macOS machine -- can you see if being on this branch of PyVistaQt fixes things for you on mac at least? pyvista/pyvistaqt#565 And maybe we'll get lucky and it'll also fix things on Linux. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[gedwald]

Thank you for your work. May be the wrong way to go about this, but maybe reveals some harmful discrepancy in my environment, but running with (I believe) the local module downloaded from git yields: (mne) ***@***.*** pyvistaqt % python Python 3.9.6 (default, Feb 3 2024, 15:58:27) [Clang 15.0.0 (clang-1500.3.9.4)] on darwin Type "help", "copyright", "credits" or "license" for more information.

>> import pyvistaqt

/Users/edwald/python_venvs/mne/lib/python3.9/site-packages/pyvista/utilities/__init__.py:69: PyVistaDeprecationWarning: The `pyvista.utilities` module has been deprecated. `conditional_decorator` is now imported as: `from pyvista.core.utilities import conditional_decorator`. warnings.warn( /Users/edwald/python_venvs/mne/lib/python3.9/site-packages/pyvista/utilities/__init__.py:69: PyVistaDeprecationWarning: The `pyvista.utilities` module has been deprecated. `threaded` is now imported as: `from pyvista.core.utilities import threaded`. warnings.warn( /Users/edwald/python_venvs/mne/lib/python3.9/site-packages/pyvista/plotting/plotting/__init__.py:23: PyVistaDeprecationWarning: The `pyvista.plotting.plotting` module has been deprecated. `BasePlotter` is now imported as: `from pyvista.plotting import BasePlotter`. warnings.warn( Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/edwald/pyvistaqt/pyvistaqt/__init__.py", line 3, in <module> from pyvistaqt.plotting import QtInteractor, MainWindow, BackgroundPlotter File "/Users/edwald/pyvistaqt/pyvistaqt/plotting.py", line 16, in <module> from pyvista.plotting.theme import rcParams ModuleNotFoundError: No module named 'pyvista.plotting.theme'

>> ^D

(the same, without the ‘pyvistaqt’ directory local, yields no errors)

…

On 22.04.2024, at 16:40, Eric Larson ***@***.***> wrote: Okay I was able to replicate on my macOS machine -- can you see if being on this branch of PyVistaQt fixes things for you on mac at least? pyvista/pyvistaqt#565 <pyvista/pyvistaqt#565> And maybe we'll get lucky and it'll also fix things on Linux. — Reply to this email directly, view it on GitHub <#12551 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC6TJBCNWA5Z54Z6JF5TMMLY6UOOTAVCNFSM6AAAAABGM5ILCWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZG4YDKMZVGI>. You are receiving this because you authored the thread.

[larsoner]

You should be able to do pip install git+https://github.com/larsoner/pyvistaqt.git@pyqt6 to install my branch

[gedwald]

This WORKS! Or, at least- the dipole bubble now appears exactly where I click with the mouse.
Thank you very much for this wizardry. Brilliant!
Tomorrow I will have the opportunity to test this on Ubuntu as well, or anything else I can contribute.

[gedwald]

The code works correctly on Ubuntu as well, with your fix.
Both my own code and your example above.
Many thanks.

[larsoner]

Great to hear!