From raw data to dSPM on SPM Faces dataset

Runs a full pipeline using MNE-Python:

• artifact removal

• averaging Epochs

• forward model computation

• source reconstruction using dSPM on the contrast : “faces - scrambled”

Note

This example does quite a bit of processing, so even on a fast machine it can take several minutes to complete.

# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#          Denis Engemann <denis.engemann@gmail.com>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import matplotlib.pyplot as plt

import mne
from mne import combine_evoked, io
from mne.datasets import spm_face
from mne.minimum_norm import apply_inverse, make_inverse_operator
from mne.preprocessing import ICA, create_eog_epochs

print(__doc__)

data_path = spm_face.data_path()
subjects_dir = data_path / "subjects"
spm_path = data_path / "MEG" / "spm"

Load and filter data, set up epochs

raw_fname = spm_path / "SPM_CTF_MEG_example_faces1_3D.ds"

raw = io.read_raw_ctf(raw_fname, preload=True)  # Take first run
# Here to save memory and time we'll downsample heavily -- this is not
# advised for real data as it can effectively jitter events!
raw.resample(120.0, npad="auto")

picks = mne.pick_types(raw.info, meg=True, exclude="bads")
raw.filter(1, 30, method="fir", fir_design="firwin")

events = mne.find_events(raw, stim_channel="UPPT001")

# plot the events to get an idea of the paradigm
mne.viz.plot_events(events, raw.info["sfreq"])

event_ids = {"faces": 1, "scrambled": 2}

tmin, tmax = -0.2, 0.6
baseline = None  # no baseline as high-pass is applied
reject = dict(mag=5e-12)

epochs = mne.Epochs(
    raw,
    events,
    event_ids,
    tmin,
    tmax,
    picks=picks,
    baseline=baseline,
    preload=True,
    reject=reject,
)

# Fit ICA, find and remove major artifacts
ica = ICA(n_components=0.95, max_iter="auto", random_state=0)
ica.fit(raw, decim=1, reject=reject)

# compute correlation scores, get bad indices sorted by score
eog_epochs = create_eog_epochs(raw, ch_name="MRT31-2908", reject=reject)
eog_inds, eog_scores = ica.find_bads_eog(eog_epochs, ch_name="MRT31-2908")
ica.plot_scores(eog_scores, eog_inds)  # see scores the selection is based on
ica.plot_components(eog_inds)  # view topographic sensitivity of components
ica.exclude += eog_inds[:1]  # we saw the 2nd ECG component looked too dipolar
ica.plot_overlay(eog_epochs.average())  # inspect artifact removal
ica.apply(epochs)  # clean data, default in place

evoked = [epochs[k].average() for k in event_ids]

contrast = combine_evoked(evoked, weights=[-1, 1])  # Faces - scrambled

evoked.append(contrast)

for e in evoked:
    e.plot(ylim=dict(mag=[-400, 400]))

plt.show()

# estimate noise covarariance
noise_cov = mne.compute_covariance(epochs, tmax=0, method="shrunk", rank=None)

Visualize fields on MEG helmet

# The transformation here was aligned using the dig-montage. It's included in
# the spm_faces dataset and is named SPM_dig_montage.fif.
trans_fname = spm_path / "SPM_CTF_MEG_example_faces1_3D_raw-trans.fif"

maps = mne.make_field_map(
    evoked[0], trans_fname, subject="spm", subjects_dir=subjects_dir, n_jobs=None
)

evoked[0].plot_field(maps, time=0.170, time_viewer=False)

Look at the whitened evoked daat

evoked[0].plot_white(noise_cov)

Compute forward model

src = subjects_dir / "spm" / "bem" / "spm-oct-6-src.fif"
bem = subjects_dir / "spm" / "bem" / "spm-5120-5120-5120-bem-sol.fif"
forward = mne.make_forward_solution(contrast.info, trans_fname, src, bem)

Compute inverse solution

snr = 3.0
lambda2 = 1.0 / snr**2
method = "dSPM"

inverse_operator = make_inverse_operator(
    contrast.info, forward, noise_cov, loose=0.2, depth=0.8
)

# Compute inverse solution on contrast
stc = apply_inverse(contrast, inverse_operator, lambda2, method, pick_ori=None)
# stc.save('spm_%s_dSPM_inverse' % contrast.comment)

# Plot contrast in 3D with mne.viz.Brain if available
brain = stc.plot(
    hemi="both",
    subjects_dir=subjects_dir,
    initial_time=0.170,
    views=["ven"],
    clim={"kind": "value", "lims": [3.0, 6.0, 9.0]},
)
# brain.save_image('dSPM_map.png')

Estimated memory usage: 0 MB