Reduce EOG artifacts through regression#

Reduce artifacts by regressing the EOG channels onto the rest of the channels and then subtracting the EOG signal.

This is a quick example to show the most basic application of the technique. See the tutorial for a more thorough explanation that demonstrates more advanced approaches.

# Author: Marijn van Vliet <w.m.vanvliet@gmail.com>
#
# License: BSD (3-clause)

Import packages and load data#

We begin as always by importing the necessary Python modules and loading some data, in this case the MNE sample dataset.

import mne
from mne.datasets import sample
from mne.preprocessing import EOGRegression
from matplotlib import pyplot as plt

print(__doc__)

data_path = sample.data_path()
raw_fname = data_path / 'MEG' / 'sample' / 'sample_audvis_filt-0-40_raw.fif'

# Read raw data
raw = mne.io.read_raw_fif(raw_fname, preload=True)
events = mne.find_events(raw, 'STI 014')

# Highpass filter to eliminate slow drifts
raw.filter(0.3, None, picks='all')
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.
Reading 0 ... 41699  =      0.000 ...   277.709 secs...
319 events found
Event IDs: [ 1  2  3  4  5 32]
Filtering raw data in 1 contiguous segment
Setting up high-pass filter at 0.3 Hz

FIR filter parameters
---------------------
Designing a one-pass, zero-phase, non-causal highpass filter:
- Windowed time-domain design (firwin) method
- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
- Lower passband edge: 0.30
- Lower transition bandwidth: 0.30 Hz (-6 dB cutoff frequency: 0.15 Hz)
- Filter length: 1653 samples (11.009 sec)

[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done   1 out of   1 | elapsed:    0.0s remaining:    0.0s
[Parallel(n_jobs=1)]: Done   2 out of   2 | elapsed:    0.0s remaining:    0.0s
[Parallel(n_jobs=1)]: Done   3 out of   3 | elapsed:    0.0s remaining:    0.0s
[Parallel(n_jobs=1)]: Done   4 out of   4 | elapsed:    0.0s remaining:    0.0s
[Parallel(n_jobs=1)]: Done 376 out of 376 | elapsed:    0.7s finished
Measurement date December 03, 2002 19:01:10 GMT
Experimenter Unknown
Participant Unknown
Digitized points 146 points
Good channels 204 Gradiometers, 102 Magnetometers, 9 Stimulus, 60 EEG, 1 EOG
Bad channels MEG 2443, EEG 053
EOG channels EOG 061
ECG channels Not available
Sampling frequency 150.15 Hz
Highpass 0.30 Hz
Lowpass 40.00 Hz
Projections PCA-v1 : off
PCA-v2 : off
PCA-v3 : off
Average EEG reference : off
Filenames sample_audvis_filt-0-40_raw.fif
Duration 00:04:38 (HH:MM:SS)


Perform regression and remove EOG#

# Fit the regression model
weights = EOGRegression().fit(raw)
raw_clean = weights.apply(raw, copy=True)

# Show the filter weights in a topomap
weights.plot()
, grad/EOG 061, mag/EOG 061, eeg/EOG 061
Created an SSP operator (subspace dimension = 4)
4 projection items activated
SSP projectors applied...

Before/after comparison#

Let’s compare the signal before and after cleaning with EOG regression. This is best visualized by extracting epochs and plotting the evoked potential.

tmin, tmax = -0.1, 0.5
event_id = {'visual/left': 3, 'visual/right': 4}
evoked_before = mne.Epochs(raw, events, event_id, tmin, tmax,
                           baseline=(tmin, 0)).average()
evoked_after = mne.Epochs(raw_clean, events, event_id, tmin, tmax,
                          baseline=(tmin, 0)).average()

# Create epochs after EOG correction
epochs_after = mne.Epochs(raw_clean, events, event_id, tmin, tmax,
                          baseline=(tmin, 0))
evoked_after = epochs_after.average()

fig, ax = plt.subplots(nrows=3, ncols=2, figsize=(10, 7),
                       sharex=True, sharey='row')
evoked_before.plot(axes=ax[:, 0], spatial_colors=True)
evoked_after.plot(axes=ax[:, 1], spatial_colors=True)
fig.subplots_adjust(top=0.905, bottom=0.09, left=0.08, right=0.975,
                    hspace=0.325, wspace=0.145)
fig.suptitle('Before --> After')
Before --> After, EEG (59 channels), EEG (59 channels), Gradiometers (203 channels), Gradiometers (203 channels), Magnetometers (102 channels), Magnetometers (102 channels)
Not setting metadata
143 matching events found
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 4)
4 projection items activated
Not setting metadata
143 matching events found
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 4)
4 projection items activated
Not setting metadata
143 matching events found
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 4)
4 projection items activated

Total running time of the script: ( 0 minutes 7.584 seconds)

Estimated memory usage: 248 MB

Gallery generated by Sphinx-Gallery