Brainstorm raw (median nerve) dataset

Here we compute the evoked from raw for the Brainstorm tutorial dataset. For comparison, see [1] and:

https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf

# Authors: Mainak Jas <mainak.jas@telecom-paristech.fr>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import numpy as np

import mne
from mne.datasets.brainstorm import bst_raw
from mne.io import read_raw_ctf

print(__doc__)

tmin, tmax, event_id = -0.1, 0.3, 2  # take right-hand somato
reject = dict(mag=4e-12, eog=250e-6)

data_path = bst_raw.data_path()

raw_path = data_path / "MEG" / "bst_raw" / "subj001_somatosensory_20111109_01_AUX-f.ds"
# Here we crop to half the length to save memory
raw = read_raw_ctf(raw_path).crop(0, 120).load_data()
raw.plot()

# set EOG channel
raw.set_channel_types({"EEG058": "eog"})
raw.set_eeg_reference("average", projection=True)

# show power line interference and remove it
raw.compute_psd(tmax=60).plot(
    average=False, amplitude=False, picks="data", exclude="bads"
)
raw.notch_filter(np.arange(60, 181, 60), fir_design="firwin")

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

# pick MEG channels
picks = mne.pick_types(
    raw.info, meg=True, eeg=False, stim=False, eog=True, exclude="bads"
)

# Compute epochs
epochs = mne.Epochs(
    raw,
    events,
    event_id,
    tmin,
    tmax,
    picks=picks,
    baseline=(None, 0),
    reject=reject,
    preload=False,
)

# compute evoked
evoked = epochs.average()

# remove physiological artifacts (eyeblinks, heartbeats) using SSP on baseline
evoked.add_proj(mne.compute_proj_evoked(evoked.copy().crop(tmax=0)))
evoked.apply_proj()

# fix stim artifact
mne.preprocessing.fix_stim_artifact(evoked)

# correct delays due to hardware (stim artifact is at 4 ms)
evoked.shift_time(-0.004)

# plot the result
evoked.plot(time_unit="s")

# show topomaps
evoked.plot_topomap(times=np.array([0.016, 0.030, 0.060, 0.070]), time_unit="s")

References

[1]

François Tadel, Sylvain Baillet, John C. Mosher, Dimitrios Pantazis, and Richard M. Leahy. Brainstorm: a user-friendly application for MEG/EEG analysis. Computational Intelligence and Neuroscience, 2011:1–13, 2011. doi:10.1155/2011/879716.

Estimated memory usage: 0 MB