Note
Go to the end to download the full example code
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
import matplotlib.pyplot as plt
import mne
from mne.datasets import spm_face
from mne.preprocessing import ICA, create_eog_epochs
from mne import io, combine_evoked
from mne.minimum_norm import make_inverse_operator, apply_inverse
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_faces%d_3D.ds"
raw = io.read_raw_ctf(raw_fname % 1, 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)
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