Compute LCMV beamformer on evoked dataΒΆ

Compute LCMV beamformer solutions on an evoked dataset for three different choices of source orientation and store the solutions in stc files for visualisation.

# Author: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)

import matplotlib.pyplot as plt
import numpy as np

import mne
from mne.datasets import sample
from mne.beamformer import lcmv

print(__doc__)

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'
label_name = 'Aud-lh'
fname_label = data_path + '/MEG/sample/labels/%s.label' % label_name
subjects_dir = data_path + '/subjects'

Get epochs

event_id, tmin, tmax = 1, -0.2, 0.5

# Setup for reading the raw data
raw = mne.io.read_raw_fif(raw_fname, preload=True)
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)

# Pick the channels of interest
raw.pick_channels([raw.ch_names[pick] for pick in picks])
# Re-normalize our empty-room projectors, so they are fine after subselection
raw.info.normalize_proj()

# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax,
                    baseline=(None, 0), preload=True, proj=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)

# Compute regularized noise and data covariances
noise_cov = mne.compute_covariance(epochs, tmin=tmin, tmax=0, method='shrunk')
data_cov = mne.compute_covariance(epochs, tmin=0.04, tmax=0.15,
                                  method='shrunk')

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=0.05,
               pick_ori=pick_ori)

    # View activation time-series
    label = mne.read_label(fname_label)
    stc_label = stc.in_label(label)
    plt.plot(1e3 * stc_label.times, np.mean(stc_label.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()

# Plot last stc in the brain in 3D with PySurfer if available
brain = stc.plot(hemi='lh', subjects_dir=subjects_dir,
                 initial_time=0.1, time_unit='s')
brain.show_view('lateral')
  • ../../_images/sphx_glr_plot_lcmv_beamformer_001.png
  • ../../_images/sphx_glr_plot_lcmv_beamformer_002.png

Out:

Opening raw data file /home/ubuntu/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Current compensation grade : 0
Reading 0 ... 166799  =      0.000 ...   277.714 secs...
72 matching events found
Created an SSP operator (subspace dimension = 3)
3 projection items activated
Loading data for 72 events and 421 original time points ...
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
16 bad epochs dropped
Reading forward solution from /home/ubuntu/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif...
    Reading a source space...
    Computing patch statistics...
    Patch information added...
    Distance information added...
    [done]
    Reading a source space...
    Computing patch statistics...
    Patch information added...
    Distance information added...
    [done]
    2 source spaces read
    Desired named matrix (kind = 3523) not available
    Read MEG forward solution (7498 sources, 306 channels, free orientations)
    Desired named matrix (kind = 3523) not available
    Read EEG forward solution (7498 sources, 60 channels, free orientations)
    MEG and EEG forward solutions combined
    Source spaces transformed to the forward solution coordinate frame
    Converting to surface-based source orientations...
    Average patch normals will be employed in the rotation to the local surface coordinates....
[done]
Estimating covariance using SHRUNK
Done.
Using cross-validation to select the best estimator.
Number of samples used : 6776
[done]
log-likelihood on unseen data (descending order):
   shrunk: -195.027
selecting best estimator: shrunk
Estimating covariance using SHRUNK
Done.
Using cross-validation to select the best estimator.
Number of samples used : 3752
[done]
log-likelihood on unseen data (descending order):
   shrunk: -201.698
selecting best estimator: shrunk
    39 out of 366 channels remain after picking
    Created an SSP operator (subspace dimension = 3)
estimated rank (mag + grad): 36
Setting small MEG eigenvalues to zero.
Not doing PCA for MEG.
combining the current components...
    39 out of 366 channels remain after picking
    Created an SSP operator (subspace dimension = 3)
estimated rank (mag + grad): 36
Setting small MEG eigenvalues to zero.
Not doing PCA for MEG.
    39 out of 366 channels remain after picking
    Created an SSP operator (subspace dimension = 3)
estimated rank (mag + grad): 36
Setting small MEG eigenvalues to zero.
Not doing PCA for MEG.
Updating smoothing matrix, be patient..
Smoothing matrix creation, step 1
Smoothing matrix creation, step 2
Smoothing matrix creation, step 3
Smoothing matrix creation, step 4
Smoothing matrix creation, step 5
Smoothing matrix creation, step 6
Smoothing matrix creation, step 7
Smoothing matrix creation, step 8
Smoothing matrix creation, step 9
Smoothing matrix creation, step 10
colormap: fmin=3.98e-01 fmid=4.49e-01 fmax=1.12e+00 transparent=1

Total running time of the script: ( 0 minutes 20.966 seconds)

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