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"""
=============================================
Compute MxNE with time-frequency sparse prior
=============================================
The TF-MxNE solver is a distributed inverse method (like dSPM or sLORETA)
that promotes focal (sparse) sources (such as dipole fitting techniques).
The benefit of this approach is that:
- it is spatio-temporal without assuming stationarity (sources properties
can vary over time)
- activations are localized in space, time and frequency in one step.
- with a built-in filtering process based on a short time Fourier
transform (STFT), data does not need to be low passed (just high pass
to make the signals zero mean).
- the solver solves a convex optimization problem, hence cannot be
trapped in local minima.
References:
A. Gramfort, D. Strohmeier, J. Haueisen, M. Hamalainen, M. Kowalski
Time-Frequency Mixed-Norm Estimates: Sparse M/EEG imaging with
non-stationary source activations
Neuroimage, Volume 70, 15 April 2013, Pages 410-422, ISSN 1053-8119,
DOI: 10.1016/j.neuroimage.2012.12.051.
A. Gramfort, D. Strohmeier, J. Haueisen, M. Hamalainen, M. Kowalski
Functional Brain Imaging with M/EEG Using Structured Sparsity in
Time-Frequency Dictionaries
Proceedings Information Processing in Medical Imaging
Lecture Notes in Computer Science, 2011, Volume 6801/2011,
600-611, DOI: 10.1007/978-3-642-22092-0_49
http://dx.doi.org/10.1007/978-3-642-22092-0_49
"""
# Author: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)
print(__doc__)
import mne
from mne.datasets import sample
from mne.minimum_norm import make_inverse_operator, apply_inverse
from mne.inverse_sparse import tf_mixed_norm
from mne.viz import plot_sparse_source_estimates
data_path = sample.data_path()
fwd_fname = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
ave_fname = data_path + '/MEG/sample/sample_audvis-no-filter-ave.fif'
cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif'
# Read noise covariance matrix
cov = mne.read_cov(cov_fname)
# Handling average file
condition = 'Left visual'
evoked = mne.read_evokeds(ave_fname, condition=condition, baseline=(None, 0))
evoked = mne.pick_channels_evoked(evoked)
# We make the window slightly larger than what you'll eventually be interested
# in ([-0.05, 0.3]) to avoid edge effects.
evoked.crop(tmin=-0.1, tmax=0.4)
# Handling forward solution
forward = mne.read_forward_solution(fwd_fname, force_fixed=False,
surf_ori=True)
cov = mne.cov.regularize(cov, evoked.info)
###############################################################################
# Run solver
# alpha_space regularization parameter is between 0 and 100 (100 is high)
alpha_space = 50. # spatial regularization parameter
# alpha_time parameter promotes temporal smoothness
# (0 means no temporal regularization)
alpha_time = 1. # temporal regularization parameter
loose, depth = 0.2, 0.9 # loose orientation & depth weighting
# Compute dSPM solution to be used as weights in MxNE
inverse_operator = make_inverse_operator(evoked.info, forward, cov,
loose=loose, depth=depth)
stc_dspm = apply_inverse(evoked, inverse_operator, lambda2=1. / 9.,
method='dSPM')
# Compute TF-MxNE inverse solution
stc, residual = tf_mixed_norm(evoked, forward, cov, alpha_space, alpha_time,
loose=loose, depth=depth, maxit=200, tol=1e-4,
weights=stc_dspm, weights_min=8., debias=True,
wsize=16, tstep=4, window=0.05,
return_residual=True)
# Crop to remove edges
stc.crop(tmin=-0.05, tmax=0.3)
evoked.crop(tmin=-0.05, tmax=0.3)
residual.crop(tmin=-0.05, tmax=0.3)
ylim = dict(eeg=[-10, 10], grad=[-200, 250], mag=[-600, 600])
picks = mne.pick_types(evoked.info, meg='grad', exclude='bads')
evoked.plot(picks=picks, ylim=ylim, proj=True,
titles=dict(grad='Evoked Response (grad)'))
picks = mne.pick_types(residual.info, meg='grad', exclude='bads')
residual.plot(picks=picks, ylim=ylim, proj=True,
titles=dict(grad='Residual (grad)'))
###############################################################################
# View in 2D and 3D ("glass" brain like 3D plot)
plot_sparse_source_estimates(forward['src'], stc, bgcolor=(1, 1, 1),
opacity=0.1, fig_name="TF-MxNE (cond %s)"
% condition, modes=['sphere'], scale_factors=[1.])
time_label = 'TF-MxNE time=%0.2f ms'
brain = stc.plot('sample', 'inflated', 'rh', fmin=10e-9, fmid=15e-9,
fmax=20e-9, time_label=time_label, smoothing_steps=5,
subjects_dir=data_path + '/subjects')
brain.show_view('medial')
brain.set_data_time_index(120)
brain.add_label("V1", color="yellow", scalar_thresh=.5, borders=True)
brain.add_label("V2", color="red", scalar_thresh=.5, borders=True)
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