Compare the different ICA algorithms in MNE#

Different ICA algorithms are fit to raw MEG data, and the corresponding maps are displayed.

# Authors: Pierre Ablin <pierreablin@gmail.com>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from time import time

import mne
from mne.datasets import sample
from mne.preprocessing import ICA

print(__doc__)

Read and preprocess the data. Preprocessing consists of:

  • MEG channel selection

  • 1-30 Hz band-pass filter

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

raw = mne.io.read_raw_fif(raw_fname).crop(0, 60).pick("meg").load_data()

reject = dict(mag=5e-12, grad=4000e-13)
raw.filter(1, 30, fir_design="firwin")
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 ... 9009  =      0.000 ...    59.999 secs...
Filtering raw data in 1 contiguous segment
Setting up band-pass filter from 1 - 30 Hz

FIR filter parameters
---------------------
Designing a one-pass, zero-phase, non-causal bandpass filter:
- Windowed time-domain design (firwin) method
- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
- Lower passband edge: 1.00
- Lower transition bandwidth: 1.00 Hz (-6 dB cutoff frequency: 0.50 Hz)
- Upper passband edge: 30.00 Hz
- Upper transition bandwidth: 7.50 Hz (-6 dB cutoff frequency: 33.75 Hz)
- Filter length: 497 samples (3.310 s)

[Parallel(n_jobs=1)]: Done  17 tasks      | elapsed:    0.0s
[Parallel(n_jobs=1)]: Done  71 tasks      | elapsed:    0.0s
[Parallel(n_jobs=1)]: Done 161 tasks      | elapsed:    0.1s
[Parallel(n_jobs=1)]: Done 287 tasks      | elapsed:    0.1s
General
Filename(s) sample_audvis_filt-0-40_raw.fif
MNE object type Raw
Measurement date 2002-12-03 at 19:01:10 UTC
Participant Unknown
Experimenter Unknown
Acquisition
Duration 00:00:60 (HH:MM:SS)
Sampling frequency 150.15 Hz
Time points 9,010
Channels
Magnetometers
Gradiometers and
Head & sensor digitization 146 points
Filters
Highpass 1.00 Hz
Lowpass 30.00 Hz
Projections PCA-v1 (off)
PCA-v2 (off)
PCA-v3 (off)


Define a function that runs ICA on the raw MEG data and plots the components

def run_ica(method, fit_params=None):
    ica = ICA(
        n_components=20,
        method=method,
        fit_params=fit_params,
        max_iter="auto",
        random_state=0,
    )
    t0 = time()
    ica.fit(raw, reject=reject)
    fit_time = time() - t0
    title = f"ICA decomposition using {method} (took {fit_time:.1f}s)"
    ica.plot_components(title=title)

FastICA

run_ica("fastica")
ICA decomposition using fastica (took 0.5s), ICA000 (mag), ICA001 (mag), ICA002 (mag), ICA003 (mag), ICA004 (mag), ICA005 (mag), ICA006 (mag), ICA007 (mag), ICA008 (mag), ICA009 (mag), ICA010 (mag), ICA011 (mag), ICA012 (mag), ICA013 (mag), ICA014 (mag), ICA015 (mag), ICA016 (mag), ICA017 (mag), ICA018 (mag), ICA019 (mag)
Fitting ICA to data using 305 channels (please be patient, this may take a while)
Selecting by number: 20 components
Fitting ICA took 0.5s.

Picard

run_ica("picard")
ICA decomposition using picard (took 1.1s), ICA000 (mag), ICA001 (mag), ICA002 (mag), ICA003 (mag), ICA004 (mag), ICA005 (mag), ICA006 (mag), ICA007 (mag), ICA008 (mag), ICA009 (mag), ICA010 (mag), ICA011 (mag), ICA012 (mag), ICA013 (mag), ICA014 (mag), ICA015 (mag), ICA016 (mag), ICA017 (mag), ICA018 (mag), ICA019 (mag)
Fitting ICA to data using 305 channels (please be patient, this may take a while)
Selecting by number: 20 components
Fitting ICA took 1.1s.

Infomax

run_ica("infomax")
ICA decomposition using infomax (took 1.5s), ICA000 (mag), ICA001 (mag), ICA002 (mag), ICA003 (mag), ICA004 (mag), ICA005 (mag), ICA006 (mag), ICA007 (mag), ICA008 (mag), ICA009 (mag), ICA010 (mag), ICA011 (mag), ICA012 (mag), ICA013 (mag), ICA014 (mag), ICA015 (mag), ICA016 (mag), ICA017 (mag), ICA018 (mag), ICA019 (mag)
Fitting ICA to data using 305 channels (please be patient, this may take a while)
Selecting by number: 20 components
Computing Infomax ICA
Fitting ICA took 1.4s.

Extended Infomax

run_ica("infomax", fit_params=dict(extended=True))
ICA decomposition using infomax (took 2.4s), ICA000 (mag), ICA001 (mag), ICA002 (mag), ICA003 (mag), ICA004 (mag), ICA005 (mag), ICA006 (mag), ICA007 (mag), ICA008 (mag), ICA009 (mag), ICA010 (mag), ICA011 (mag), ICA012 (mag), ICA013 (mag), ICA014 (mag), ICA015 (mag), ICA016 (mag), ICA017 (mag), ICA018 (mag), ICA019 (mag)
Fitting ICA to data using 305 channels (please be patient, this may take a while)
Selecting by number: 20 components
Computing Extended Infomax ICA
Fitting ICA took 2.4s.

Total running time of the script: (0 minutes 25.235 seconds)

Estimated memory usage: 29 MB

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