def test_get_montage_volume_labels():
"""Test finding ROI labels near montage channel locations."""
ch_coords = np.array([[-8.7040273, 17.99938754, 10.29604017],
[-14.03007764, 19.69978401, 12.07236939],
[-21.1130506, 21.98310911, 13.25658887]])
ch_pos = dict(zip(['1', '2', '3'], ch_coords / 1000)) # mm -> m
montage = make_dig_montage(ch_pos, coord_frame='mri')
labels, colors = get_montage_volume_labels(montage,
'sample',
subjects_dir,
aseg='aseg',
dist=1)
assert labels == {
'1': ['Unknown'],
'2': ['Left-Cerebral-Cortex'],
'3': ['Left-Cerebral-Cortex']
}
assert 'Unknown' in colors
assert 'Left-Cerebral-Cortex' in colors
np.testing.assert_almost_equal(
colors['Left-Cerebral-Cortex'],
(0.803921568627451, 0.24313725490196078, 0.3058823529411765, 1.0))
np.testing.assert_almost_equal(colors['Unknown'], (0.0, 0.0, 0.0, 1.0))
# test inputs
with pytest.raises(RuntimeError,
match='`aseg` file path must end with "aseg"'):
get_montage_volume_labels(montage, 'sample', subjects_dir, aseg='foo')
fail_montage = make_dig_montage(ch_pos, coord_frame='head')
with pytest.raises(RuntimeError, match='Coordinate frame not supported'):
get_montage_volume_labels(fail_montage,
'sample',
subjects_dir,
aseg='aseg')
fig = mne.viz.plot_alignment(epochs.info,
trans,
'fsaverage',
subjects_dir=subjects_dir,
show_axes=True,
surfaces=['pial', 'head'],
coord_frame='mri')
# %%
# Let's also look at which regions of interest are nearby our electrode
# contacts.
aseg = 'aparc+aseg' # parcellation/anatomical segmentation atlas
labels, colors = mne.get_montage_volume_labels(montage,
'fsaverage',
subjects_dir=subjects_dir,
aseg=aseg)
# separate by electrodes which have names like LAMY 1
electrodes = set([
''.join([lttr for lttr in ch_name if not lttr.isdigit() and lttr != ' '])
for ch_name in montage.ch_names
])
print(f'Electrodes in the dataset: {electrodes}')
electrodes = ('LPM', 'LSMA') # choose two for this example
for elec in electrodes:
picks = [ch_name for ch_name in epochs.ch_names if elec in ch_name]
fig = plt.figure(num=None, figsize=(8, 8), facecolor='black')
mne.viz.plot_channel_labels_circle(labels, colors, picks=picks, fig=fig)
fig.text(0.3, 0.9, 'Anatomical Labels', color='white')
