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"""
======================
Working with ECoG data
======================
MNE supports working with more than just MEG and EEG data. Here we show some
of the functions that can be used to facilitate working with
electrocorticography (ECoG) data.
"""
# Authors: Eric Larson <larson.eric.d@gmail.com>
# Chris Holdgraf <choldgraf@gmail.com>
#
# License: BSD (3-clause)
import numpy as np
import matplotlib.pyplot as plt
from scipy.io import loadmat
import mne
from mne.viz import plot_alignment, snapshot_brain_montage
print(__doc__)
###############################################################################
# Let's load some ECoG electrode locations and names, and turn them into
# a :class:`mne.channels.DigMontage` class.
mat = loadmat(mne.datasets.misc.data_path() + '/ecog/sample_ecog.mat')
ch_names = mat['ch_names'].tolist()
elec = mat['elec'] # electrode positions given in meters
# Now we make a montage stating that the sEEG contacts are in head
# coordinate system (although they are in MRI). This is compensated
# by the fact that below we do not specicty a trans file so the Head<->MRI
# transform is the identity.
montage = mne.channels.make_dig_montage(ch_pos=dict(zip(ch_names, elec)),
coord_frame='head')
print('Created %s channel positions' % len(ch_names))
###############################################################################
# Now that we have our electrode positions in MRI coordinates, we can create
# our measurement info structure.
info = mne.create_info(ch_names, 1000., 'ecog', montage=montage)
###############################################################################
# We can then plot the locations of our electrodes on our subject's brain.
#
# .. note:: These are not real electrodes for this subject, so they
# do not align to the cortical surface perfectly.
subjects_dir = mne.datasets.sample.data_path() + '/subjects'
fig = plot_alignment(info, subject='sample', subjects_dir=subjects_dir,
surfaces=['pial'])
mne.viz.set_3d_view(fig, 200, 70)
###############################################################################
# Sometimes it is useful to make a scatterplot for the current figure view.
# This is best accomplished with matplotlib. We can capture an image of the
# current mayavi view, along with the xy position of each electrode, with the
# `snapshot_brain_montage` function.
# We'll once again plot the surface, then take a snapshot.
fig_scatter = plot_alignment(info, subject='sample', subjects_dir=subjects_dir,
surfaces='pial')
mne.viz.set_3d_view(fig_scatter, 200, 70)
xy, im = snapshot_brain_montage(fig_scatter, montage)
# Convert from a dictionary to array to plot
xy_pts = np.vstack([xy[ch] for ch in info['ch_names']])
# Define an arbitrary "activity" pattern for viz
activity = np.linspace(100, 200, xy_pts.shape[0])
# This allows us to use matplotlib to create arbitrary 2d scatterplots
_, ax = plt.subplots(figsize=(10, 10))
ax.imshow(im)
ax.scatter(*xy_pts.T, c=activity, s=200, cmap='coolwarm')
ax.set_axis_off()
plt.show()
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