Description
Description of the problem
Hi and thank you for all the effort put into MNE-Python! Unfortunately, I ran into a problem when trying to plot borders of any region of the Desikan-Killiany parcellation on the flat brain surface. Somewhat surprisingly to me, plotting the parcellation as a whole works fine, although it also requires showing borders of all regions. Plotting the whole region (borders=False) also works, the problem only occurs with borders=True or borders set to an integer.
I would be happy to fix the issue but it might take a while for me to figure out the cause. If you have any hints about what went wrong, they would help a lot :)
Steps to reproduce
import mne
from mne.datasets import sample
subjects_dir = sample.data_path() / "subjects"
subject = "fsaverage"
labels = mne.read_labels_from_annot(subject, "aparc", subjects_dir=subjects_dir)
Brain = mne.viz.get_brain_class()
brain = Brain(subject=subject, hemi="lh", surf="flat")
# brain.add_annotation("aparc") # works fine
# brain.add_label(labels[0], borders=False) # works fine
brain.add_label(labels[0], borders=True) # crashes
brain._renderer.plotter.app.exec()Link to data
No response
Expected results
A Pyvista figure of the flat surface of the left hemisphere with borders of one label (bankssts-lh) shown
Actual results
Error message:
Traceback (most recent call last):
File "/home/willenjoy/Projects/roiextract-simulations/scripts/misc/bugs/mne_viz_brain_add_label_flat.py", line 14, in <module>
brain.add_label(labels[0], borders=True) # crashes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/willenjoy/miniforge3/envs/roiextract-simulations/lib/python3.12/site-packages/mne/viz/_brain/_brain.py", line 2265, in add_label
keep_idx = _mesh_borders(self.geo[hemi].faces, scalars)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/willenjoy/miniforge3/envs/roiextract-simulations/lib/python3.12/site-packages/mne/surface.py", line 1929, in _mesh_borders
edges = mesh_edges(tris)
^^^^^^^^^^^^^^^^
File "/home/willenjoy/miniforge3/envs/roiextract-simulations/lib/python3.12/site-packages/mne/surface.py", line 1713, in mesh_edges
return _mesh_edges(tris=tris)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/willenjoy/miniforge3/envs/roiextract-simulations/lib/python3.12/site-packages/mne/surface.py", line 1719, in _mesh_edges
raise ValueError("Cannot compute adjacency on a selection of triangles.")
ValueError: Cannot compute adjacency on a selection of triangles.
Additional information
Platform Linux-6.8.0-57-generic-x86_64-with-glibc2.35
Python 3.12.0 | packaged by conda-forge | (main, Oct 3 2023, 08:43:22) [GCC 12.3.0]
Executable /home/willenjoy/miniforge3/envs/roiextract-simulations/bin/python
CPU 12th Gen Intel(R) Core(TM) i7-1255U (12 cores)
Memory 15.3 GiB
Core
├☑ mne 1.9.0 (latest release)
├☑ numpy 1.26.2 (OpenBLAS 0.3.23.dev with 12 threads)
├☑ scipy 1.14.1
└☑ matplotlib 3.8.2 (backend=QtAgg)
Numerical (optional)
├☑ sklearn 1.3.2
├☑ numba 0.61.0
├☑ nibabel 5.2.0
├☑ pandas 2.1.4
└☐ unavailable nilearn, dipy, openmeeg, cupy, h5io, h5py
Visualization (optional)
├☑ pyvista 0.43.1 (OpenGL 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 via Mesa Intel(R) Graphics (ADL GT2))
├☑ pyvistaqt 0.11.0
├☑ vtk 9.3.0
├☑ qtpy 2.4.1 (PyQt6=6.8.1)
└☐ unavailable ipympl, pyqtgraph, mne-qt-browser, ipywidgets, trame_client, trame_server, trame_vtk, trame_vuetify
Ecosystem (optional)
├☑ mne-bids 0.16.0
├☑ mne-connectivity 0.7.0
└☐ unavailable mne-nirs, mne-features, mne-icalabel, mne-bids-pipeline, neo, eeglabio, edfio, mffpy, pybv