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This example shows how to load raw data and apply some EEG referencing schemes.
# Authors: Marijn van Vliet <w.m.vanvliet@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)
import mne
from mne.datasets import sample
from matplotlib import pyplot as plt
print(__doc__)
# Setup for reading the raw data
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
event_id, tmin, tmax = 1, -0.2, 0.5
# Read the raw data
raw = mne.io.read_raw_fif(raw_fname, preload=True)
events = mne.read_events(event_fname)
# The EEG channels will be plotted to visualize the difference in referencing
# schemes.
picks = mne.pick_types(raw.info, meg=False, eeg=True, eog=True, exclude='bads')
Out:
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw.fif...
Read a total of 4 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Average EEG reference (1 x 60) idle
Range : 6450 ... 48149 = 42.956 ... 320.665 secs
Ready.
Current compensation grade : 0
Reading 0 ... 41699 = 0.000 ... 277.709 secs...
We will now apply different EEG referencing schemes and plot the resulting
evoked potentials. Note that when we construct epochs with mne.Epochs, we
supply the proj=True argument. This means that any available projectors
are applied automatically. Specifically, if there is an average reference
projector set by raw.set_eeg_reference('average', projection=True), MNE
applies this projector when creating epochs.
reject = dict(eog=150e-6)
epochs_params = dict(events=events, event_id=event_id, tmin=tmin, tmax=tmax,
picks=picks, reject=reject, proj=True)
fig, (ax1, ax2, ax3) = plt.subplots(nrows=3, ncols=1, sharex=True)
# No reference. This assumes that the EEG has already been referenced properly.
# This explicitly prevents MNE from adding a default EEG reference. Any average
# reference projector is automatically removed.
raw.set_eeg_reference([])
evoked_no_ref = mne.Epochs(raw, **epochs_params).average()
evoked_no_ref.plot(axes=ax1, titles=dict(eeg='Original reference'), show=False,
time_unit='s')
# Average reference. This is normally added by default, but can also be added
# explicitly.
raw.set_eeg_reference('average', projection=True)
evoked_car = mne.Epochs(raw, **epochs_params).average()
evoked_car.plot(axes=ax2, titles=dict(eeg='Average reference'), show=False,
time_unit='s')
# Re-reference from an average reference to the mean of channels EEG 001 and
# EEG 002.
raw.set_eeg_reference(['EEG 001', 'EEG 002'])
evoked_custom = mne.Epochs(raw, **epochs_params).average()
evoked_custom.plot(axes=ax3, titles=dict(eeg='Custom reference'),
time_unit='s')
Out:
EEG data marked as already having the desired reference. Preventing automatic future re-referencing to an average reference.
Removing existing average EEG reference projection.
Created an SSP operator (subspace dimension = 3)
72 matching events found
Applying baseline correction (mode: mean)
Not setting metadata
3 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Adding average EEG reference projection.
1 projection items deactivated
Average reference projection was added, but has not been applied yet. Use the apply_proj method to apply it.
72 matching events found
Applying baseline correction (mode: mean)
Not setting metadata
Created an SSP operator (subspace dimension = 1)
4 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Applying a custom EEG reference.
Removing existing average EEG reference projection.
Created an SSP operator (subspace dimension = 3)
72 matching events found
Applying baseline correction (mode: mean)
Not setting metadata
3 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Total running time of the script: ( 0 minutes 2.177 seconds)