Re-referencing the EEG signalΒΆ

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/ubuntu/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...

Apply different EEG referencing schemes and plot the resulting evokeds.

reject = dict(eeg=180e-6, eog=150e-6)
epochs_params = dict(events=events, event_id=event_id, tmin=tmin, tmax=tmax,
                     picks=picks, reject=reject)

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.
raw.set_eeg_reference([])
evoked_no_ref = mne.Epochs(raw, **epochs_params).average()

evoked_no_ref.plot(axes=ax1, titles=dict(eeg='EEG Original reference'))

# Average reference. This is normally added by default, but can also be added
# explicitly.
raw.set_eeg_reference()
evoked_car = mne.Epochs(raw, **epochs_params).average()

evoked_car.plot(axes=ax2, titles=dict(eeg='EEG Average reference'))

# 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='EEG Custom reference'))
../../_images/sphx_glr_plot_rereference_eeg_001.png

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.
72 matching events found
3 projection items activated
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EEG : [u'EEG 007']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EEG : [u'EEG 001', u'EEG 002', u'EEG 003', u'EEG 007']
    Rejecting  epoch based on EEG : [u'EEG 001', u'EEG 002', u'EEG 003', u'EEG 007']
Adding average EEG reference projection.
1 projection items deactivated
Average reference projection was added, but hasn't been applied yet. Use the .apply_proj() method function to apply projections.
72 matching events found
Created an SSP operator (subspace dimension = 1)
4 projection items activated
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
Applying a custom EEG reference.
Removing existing average EEG reference projection.
72 matching events found
3 projection items activated
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']
    Rejecting  epoch based on EOG : [u'EOG 061']

Total running time of the script: ( 0 minutes 2.099 seconds)

Generated by Sphinx-Gallery