Compute iterative reweighted TF-MxNE with multiscale time-frequency dictionary

The iterative reweighted TF-MxNE solver is a distributed inverse method based on the TF-MxNE solver, which promotes focal (sparse) sources [1]. The benefits of this approach are that:

• it is spatio-temporal without assuming stationarity (source properties can vary over time),

• activations are localized in space, time, and frequency in one step,

• the solver uses non-convex penalties in the TF domain, which results in a solution less biased towards zero than when simple TF-MxNE is used,

• using a multiscale dictionary allows to capture short transient activations along with slower brain waves [2].

# Author: Mathurin Massias <mathurin.massias@gmail.com>
#         Yousra Bekhti <yousra.bekhti@gmail.com>
#         Daniel Strohmeier <daniel.strohmeier@tu-ilmenau.de>
#         Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import mne
from mne.datasets import somato
from mne.inverse_sparse import make_stc_from_dipoles, tf_mixed_norm
from mne.viz import plot_sparse_source_estimates

print(__doc__)

Load somatosensory MEG data

data_path = somato.data_path()
subject = "01"
task = "somato"
raw_fname = data_path / f"sub-{subject}" / "meg" / f"sub-{subject}_task-{task}_meg.fif"
fwd_fname = (
    data_path / "derivatives" / f"sub-{subject}" / f"sub-{subject}_task-{task}-fwd.fif"
)

# Read evoked
raw = mne.io.read_raw_fif(raw_fname)
raw.pick(picks=["meg", "eog", "stim"])
events = mne.find_events(raw, stim_channel="STI 014")

reject = dict(grad=4000e-13, eog=350e-6)
event_id, tmin, tmax = dict(unknown=1), -0.5, 0.5
epochs = mne.Epochs(
    raw, events, event_id, tmin, tmax, reject=reject, baseline=(None, 0)
)
evoked = epochs.average()

evoked.crop(tmin=0.0, tmax=0.2)

# Compute noise covariance matrix
cov = mne.compute_covariance(epochs, rank="info", tmax=0.0)
del epochs, raw

# Handling forward solution
forward = mne.read_forward_solution(fwd_fname)

Run iterative reweighted multidict TF-MxNE solver

alpha, l1_ratio = 20, 0.05
loose, depth = 0.9, 1.0
# Use a multiscale time-frequency dictionary
wsize, tstep = [4, 16], [2, 4]


n_tfmxne_iter = 10
# Compute TF-MxNE inverse solution with dipole output
dipoles, residual = tf_mixed_norm(
    evoked,
    forward,
    cov,
    alpha=alpha,
    l1_ratio=l1_ratio,
    n_tfmxne_iter=n_tfmxne_iter,
    loose=loose,
    depth=depth,
    tol=1e-3,
    wsize=wsize,
    tstep=tstep,
    return_as_dipoles=True,
    return_residual=True,
)

Generate stc from dipoles

stc = make_stc_from_dipoles(dipoles, forward["src"])
plot_sparse_source_estimates(
    forward["src"],
    stc,
    bgcolor=(1, 1, 1),
    opacity=0.1,
    fig_name=f"irTF-MxNE (cond {evoked.comment})",
)

Show the evoked response and the residual for gradiometers

ylim = dict(grad=[-300, 300])
evoked.copy().pick(picks="grad").plot(
    titles=dict(grad="Evoked Response: Gradiometers"), ylim=ylim
)
residual.copy().pick(picks="grad").plot(
    titles=dict(grad="Residuals: Gradiometers"), ylim=ylim
)

References

[1]

Daniel Strohmeier, Alexandre Gramfort, and Jens Haueisen. MEG/EEG Source Imaging with a Non-Convex Penalty in the Time-Frequency Domain. In 2015 International Workshop on Pattern Recognition in NeuroImaging, 21–24. 2015. doi:10.1109/PRNI.2015.14.

[2]

Yousra Bekhti, Daniel Strohmeier, Mainak Jas, Roland Badeau, and Alexandre Gramfort. M/EEG source localization with multi-scale time-frequency dictionaries. In Proceedings of PRNI-2016, 1–4. Trento, 2016. IEEE. doi:10.1109/PRNI.2016.7552337.

Estimated memory usage: 0 MB