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"""
============================
Brainstorm tutorial datasets
============================
Here we compute the evoked from raw for the Brainstorm
tutorial dataset. For comparison, see [1]_ and:
http://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf
References
----------
.. [1] Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM.
Brainstorm: A User-Friendly Application for MEG/EEG Analysis.
Computational Intelligence and Neuroscience, vol. 2011, Article ID
879716, 13 pages, 2011. doi:10.1155/2011/879716
"""
# Authors: Mainak Jas <mainak.jas@telecom-paristech.fr>
#
# License: BSD (3-clause)
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')
raw = read_raw_ctf(raw_path, preload=True)
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.plot_psd(tmax=60., average=False)
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')
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