Removing muscle ICA components#

Gross movements produce widespread high-frequency activity across all channels that is usually not recoverable and so the epoch must be rejected as shown in Annotate muscle artifacts. More ubiquitously than gross movements, muscle artifact is produced during postural maintenance. This is more appropriately removed by ICA otherwise there wouldn’t be any epochs left! Note that muscle artifacts of this kind are much more pronounced in EEG than they are in MEG.

# Authors: Alex Rockhill <aprockhill@mailbox.org>
#
# License: BSD-3-Clause
import mne

data_path = mne.datasets.sample.data_path()
raw_fname = data_path / 'MEG' / 'sample' / 'sample_audvis_raw.fif'
raw = mne.io.read_raw_fif(raw_fname)
raw.crop(tmin=100, tmax=130)  # take 30 seconds for speed

# pick only EEG channels, muscle artifact is basically not picked up by MEG
# if you have a simultaneous recording, you may want to do ICA on MEG and EEG
# separately
raw.pick_types(eeg=True)

# ICA works best with a highpass filter applied
raw.load_data()
raw.filter(l_freq=1., h_freq=None)
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Removing projector <Projection | PCA-v1, active : False, n_channels : 102>
Removing projector <Projection | PCA-v2, active : False, n_channels : 102>
Removing projector <Projection | PCA-v3, active : False, n_channels : 102>
Reading 0 ... 18019  =      0.000 ...    30.001 secs...
Filtering raw data in 1 contiguous segment
Setting up high-pass filter at 1 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: 1.00
- Lower transition bandwidth: 1.00 Hz (-6 dB cutoff frequency: 0.50 Hz)
- Filter length: 1983 samples (3.302 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  59 out of  59 | elapsed:    0.1s finished
Measurement date December 03, 2002 19:01:10 GMT
Experimenter MEG
Participant Unknown
Digitized points 146 points
Good channels 59 EEG
Bad channels None
EOG channels Not available
ECG channels Not available
Sampling frequency 600.61 Hz
Highpass 1.00 Hz
Lowpass 172.18 Hz
Filenames sample_audvis_raw.fif
Duration 00:00:30 (HH:MM:SS)


Run ICA

ica = mne.preprocessing.ICA(
    n_components=15, method='picard', max_iter='auto', random_state=97)
ica.fit(raw)
Fitting ICA to data using 59 channels (please be patient, this may take a while)
Selecting by number: 15 components
Fitting ICA took 1.1s.
Method picard
Fit 36 iterations on raw data (18020 samples)
ICA components 15
Explained variance 96.0 %
Available PCA components 59
Channel types eeg
ICA components marked for exclusion


Remove components with postural muscle artifact using ICA

Raw plot
Creating RawArray with float64 data, n_channels=15, n_times=18020
    Range : 85861 ... 103880 =    142.955 ...   172.956 secs
Ready.

By inspection, let’s select out the muscle-artifact components based on [1] manually.

The criteria are:

  • Positive slope of log-log power spectrum between 7 and 75 Hz (here just flat because it’s not in log-log)

  • Peripheral focus or dipole/multi-pole foci (the blue and red blobs in the topomap are far from the vertex where the most muscle is)

  • Single focal point (low spatial smoothness; there is just one focus of the topomap compared to components like the first ones that are more likely neural which spread across the topomap)

The other attribute worth noting is that the time course in mne.preprocessing.ICA.plot_sources() looks like EMG; you can see spikes when each motor unit fires so that the time course looks fuzzy and sometimes has large spikes that are often at regular intervals.

ICA component 13 is a textbook example of what muscle artifact looks like. The focus of the topomap for this component is right on the temporalis muscle near the ears. There is also a minimum in the power spectrum at around 10 Hz, then a maximum at around 25 Hz, generally resulting in a positive slope in log-log units; this is a very typical pattern for muscle artifact.

muscle_idx = [6, 7, 8, 9, 10, 11, 12, 13, 14]
ica.plot_properties(raw, picks=muscle_idx, log_scale=True)

# first, remove blinks and heartbeat to compare
blink_idx = [0]
heartbeat_idx = [5]
ica.apply(raw, exclude=blink_idx + heartbeat_idx)
ica.plot_overlay(raw, exclude=muscle_idx)
  • ICA006, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA007, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA008, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA009, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA010, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA011, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA012, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA013, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA014, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • Signals before (red) and after (black) cleaning, Raw data, Average across channels (EEG)
    Using multitaper spectrum estimation with 7 DPSS windows
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
15 matching events found
No baseline correction applied
0 projection items activated
Applying ICA to Raw instance
    Transforming to ICA space (15 components)
    Zeroing out 2 ICA components
    Projecting back using 59 PCA components
Applying ICA to Raw instance
    Transforming to ICA space (15 components)
    Zeroing out 9 ICA components
    Projecting back using 59 PCA components

Finally, let’s try an automated algorithm to find muscle components and ensure that it gets the same components we did manually.

muscle_idx_auto, scores = ica.find_bads_muscle(raw)
ica.plot_scores(scores, exclude=muscle_idx_auto)
print(f'Manually found muscle artifact ICA components:      {muscle_idx}\n'
      f'Automatically found muscle artifact ICA components: {muscle_idx_auto}')
ICA component scores
Effective window size : 0.426 (s)
[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   1 out of   1 | elapsed:    0.0s finished
Manually found muscle artifact ICA components:      [6, 7, 8, 9, 10, 11, 12, 13, 14]
Automatically found muscle artifact ICA components: [6, 7, 8, 9, 10, 11, 12, 13, 14]

Let’s now replicate this on the EEGBCI dataset#

for sub in (1, 2):
    raw = mne.io.read_raw_edf(
        mne.datasets.eegbci.load_data(subject=sub, runs=(1,))[0], preload=True)
    mne.datasets.eegbci.standardize(raw)  # set channel names
    montage = mne.channels.make_standard_montage('standard_1005')
    raw.set_montage(montage)
    raw.filter(l_freq=1., h_freq=None)

    # Run ICA
    ica = mne.preprocessing.ICA(
        n_components=15, method='picard', max_iter='auto', random_state=97)
    ica.fit(raw)
    ica.plot_sources(raw)
    muscle_idx_auto, scores = ica.find_bads_muscle(raw)
    ica.plot_properties(raw, picks=muscle_idx_auto, log_scale=True)
    ica.plot_scores(scores, exclude=muscle_idx_auto)

    print(f'Manually found muscle artifact ICA components:      {muscle_idx}\n'
          'Automatically found muscle artifact ICA components: '
          f'{muscle_idx_auto}')
  • ICA009, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA component scores
  • ICA005, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA010, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA012, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA013, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA014, Segment image and ERP/ERF, Spectrum, Dropped segments: 0.00 %
  • ICA component scores
  • Raw plots
  • Raw plots
Exception ignored in: <_io.FileIO name='/home/circleci/project/mne/data/eegbci_checksums.txt' mode='rb' closefd=True>
Traceback (most recent call last):
  File "<decorator-gen-544>", line 12, in load_data
ResourceWarning: unclosed file <_io.BufferedReader name='/home/circleci/project/mne/data/eegbci_checksums.txt'>
Extracting EDF parameters from /home/circleci/mne_data/MNE-eegbci-data/files/eegmmidb/1.0.0/S001/S001R01.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Reading 0 ... 9759  =      0.000 ...    60.994 secs...
Filtering raw data in 1 contiguous segment
Setting up high-pass filter at 1 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: 1.00
- Lower transition bandwidth: 1.00 Hz (-6 dB cutoff frequency: 0.50 Hz)
- Filter length: 529 samples (3.306 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  64 out of  64 | elapsed:    0.0s finished
Fitting ICA to data using 64 channels (please be patient, this may take a while)
Selecting by number: 15 components
Fitting ICA took 0.7s.
Creating RawArray with float64 data, n_channels=15, n_times=9760
    Range : 0 ... 9759 =      0.000 ...    60.994 secs
Ready.
Effective window size : 1.600 (s)
[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   1 out of   1 | elapsed:    0.0s finished
    Using multitaper spectrum estimation with 7 DPSS windows
Not setting metadata
30 matching events found
No baseline correction applied
0 projection items activated
Manually found muscle artifact ICA components:      [6, 7, 8, 9, 10, 11, 12, 13, 14]
Automatically found muscle artifact ICA components: [9]
Exception ignored in: <_io.FileIO name='/home/circleci/project/mne/data/eegbci_checksums.txt' mode='rb' closefd=True>
Traceback (most recent call last):
  File "<decorator-gen-544>", line 12, in load_data
ResourceWarning: unclosed file <_io.BufferedReader name='/home/circleci/project/mne/data/eegbci_checksums.txt'>
Extracting EDF parameters from /home/circleci/mne_data/MNE-eegbci-data/files/eegmmidb/1.0.0/S002/S002R01.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Reading 0 ... 9759  =      0.000 ...    60.994 secs...
Filtering raw data in 1 contiguous segment
Setting up high-pass filter at 1 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: 1.00
- Lower transition bandwidth: 1.00 Hz (-6 dB cutoff frequency: 0.50 Hz)
- Filter length: 529 samples (3.306 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  64 out of  64 | elapsed:    0.0s finished
Fitting ICA to data using 64 channels (please be patient, this may take a while)
Selecting by number: 15 components
Fitting ICA took 0.6s.
Creating RawArray with float64 data, n_channels=15, n_times=9760
    Range : 0 ... 9759 =      0.000 ...    60.994 secs
Ready.
Effective window size : 1.600 (s)
[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   1 out of   1 | elapsed:    0.0s finished
    Using multitaper spectrum estimation with 7 DPSS windows
Not setting metadata
30 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
30 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
30 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
30 matching events found
No baseline correction applied
0 projection items activated
Not setting metadata
30 matching events found
No baseline correction applied
0 projection items activated
Manually found muscle artifact ICA components:      [6, 7, 8, 9, 10, 11, 12, 13, 14]
Automatically found muscle artifact ICA components: [5, 10, 12, 13, 14]

References#

Total running time of the script: ( 0 minutes 31.436 seconds)

Estimated memory usage: 20 MB

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