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"""
======================================
Compute LCMV beamformer on evoked data
======================================
Compute LCMV beamformer solutions on evoked dataset for three different choices
of source orientation and stores the solutions in stc files for visualisation.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)
print(__doc__)
import matplotlib.pyplot as plt
import numpy as np
import mne
from mne.datasets import sample
from mne.io import Raw
from mne.beamformer import lcmv
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_raw-eve.fif'
fname_fwd = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
fname_cov = data_path + '/MEG/sample/sample_audvis-cov.fif'
label_name = 'Aud-lh'
fname_label = data_path + '/MEG/sample/labels/%s.label' % label_name
###############################################################################
# Get epochs
event_id, tmin, tmax = 1, -0.2, 0.5
# Setup for reading the raw data
raw = Raw(raw_fname)
raw.info['bads'] = ['MEG 2443', 'EEG 053'] # 2 bads channels
events = mne.read_events(event_fname)
# Set up pick list: EEG + MEG - bad channels (modify to your needs)
left_temporal_channels = mne.read_selection('Left-temporal')
picks = mne.pick_types(raw.info, meg=True, eeg=False, stim=True, eog=True,
exclude='bads', selection=left_temporal_channels)
# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
picks=picks, baseline=(None, 0), preload=True,
reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
evoked = epochs.average()
forward = mne.read_forward_solution(fname_fwd, surf_ori=True)
noise_cov = mne.read_cov(fname_cov)
noise_cov = mne.cov.regularize(noise_cov, evoked.info,
mag=0.05, grad=0.05, eeg=0.1, proj=True)
data_cov = mne.compute_covariance(epochs, tmin=0.04, tmax=0.15)
plt.close('all')
pick_oris = [None, 'normal', 'max-power']
names = ['free', 'normal', 'max-power']
descriptions = ['Free orientation', 'Normal orientation', 'Max-power '
'orientation']
colors = ['b', 'k', 'r']
for pick_ori, name, desc, color in zip(pick_oris, names, descriptions, colors):
stc = lcmv(evoked, forward, noise_cov, data_cov, reg=0.01,
pick_ori=pick_ori)
# Save result in stc files
stc.save('lcmv-' + name)
# View activation time-series
data, times, _ = mne.label_time_courses(fname_label, "lcmv-" + name +
"-lh.stc")
plt.plot(1e3 * times, np.mean(data, axis=0), color, hold=True, label=desc)
plt.xlabel('Time (ms)')
plt.ylabel('LCMV value')
plt.ylim(-0.8, 2.2)
plt.title('LCMV in %s' % label_name)
plt.legend()
plt.show()
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