Note

Click here to download the full example code

# Time-frequency beamforming using DICS¶

Compute DICS source power 1 in a grid of time-frequency windows.

## References¶

- 1
Dalal et al. Five-dimensional neuroimaging: Localization of the time-frequency dynamics of cortical activity. NeuroImage (2008) vol. 40 (4) pp. 1686-1700

```
# Author: Roman Goj <roman.goj@gmail.com>
#
# License: BSD (3-clause)
import mne
from mne.event import make_fixed_length_events
from mne.datasets import sample
from mne.time_frequency import csd_fourier
from mne.beamformer import tf_dics
from mne.viz import plot_source_spectrogram
print(__doc__)
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
noise_fname = data_path + '/MEG/sample/ernoise_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_raw-eve.fif'
fname_fwd = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
subjects_dir = data_path + '/subjects'
label_name = 'Aud-lh'
fname_label = data_path + '/MEG/sample/labels/%s.label' % label_name
```

Out:

```
```

Read raw data

```
raw = mne.io.read_raw_fif(raw_fname, preload=True)
raw.info['bads'] = ['MEG 2443'] # 1 bad MEG channel
# Pick a selection of magnetometer channels. A subset of all channels was used
# to speed up the example. For a solution based on all MEG channels use
# meg=True, selection=None and add mag=4e-12 to the reject dictionary.
left_temporal_channels = mne.read_selection('Left-temporal')
picks = mne.pick_types(raw.info, meg='mag', eeg=False, eog=False,
stim=False, exclude='bads',
selection=left_temporal_channels)
raw.pick_channels([raw.ch_names[pick] for pick in picks])
reject = dict(mag=4e-12)
# Re-normalize our empty-room projectors, which should be fine after
# subselection
raw.info.normalize_proj()
# Setting time windows. Note that tmin and tmax are set so that time-frequency
# beamforming will be performed for a wider range of time points than will
# later be displayed on the final spectrogram. This ensures that all time bins
# displayed represent an average of an equal number of time windows.
tmin, tmax, tstep = -0.5, 0.75, 0.05 # s
tmin_plot, tmax_plot = -0.3, 0.5 # s
# Read epochs
event_id = 1
events = mne.read_events(event_fname)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax,
baseline=None, preload=True, proj=True, reject=reject)
# Read empty room noise raw data
raw_noise = mne.io.read_raw_fif(noise_fname, preload=True)
raw_noise.info['bads'] = ['MEG 2443'] # 1 bad MEG channel
raw_noise.pick_channels([raw_noise.ch_names[pick] for pick in picks])
raw_noise.info.normalize_proj()
# Create noise epochs and make sure the number of noise epochs corresponds to
# the number of data epochs
events_noise = make_fixed_length_events(raw_noise, event_id)
epochs_noise = mne.Epochs(raw_noise, events_noise, event_id, tmin_plot,
tmax_plot, baseline=None, preload=True, proj=True,
reject=reject)
epochs_noise.info.normalize_proj()
epochs_noise.apply_proj()
# then make sure the number of epochs is the same
epochs_noise = epochs_noise[:len(epochs.events)]
# Read forward operator
forward = mne.read_forward_solution(fname_fwd)
# Read label
label = mne.read_label(fname_label)
```

Out:

```
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.
Current compensation grade : 0
Reading 0 ... 166799 = 0.000 ... 277.714 secs...
72 matching events found
No baseline correction applied
Not setting metadata
Created an SSP operator (subspace dimension = 3)
3 projection items activated
Loading data for 72 events and 751 original time points ...
0 bad epochs dropped
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
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 : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Current compensation grade : 0
Reading 0 ... 66067 = 0.000 ... 109.999 secs...
110 matching events found
No baseline correction applied
Not setting metadata
Created an SSP operator (subspace dimension = 3)
3 projection items activated
Loading data for 110 events and 481 original time points ...
1 bad epochs dropped
Projections have already been applied. Setting proj attribute to True.
Reading forward solution from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif...
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
Desired named matrix (kind = 3523) not available
Read MEG forward solution (7498 sources, 306 channels, free orientations)
Desired named matrix (kind = 3523) not available
Read EEG forward solution (7498 sources, 60 channels, free orientations)
MEG and EEG forward solutions combined
Source spaces transformed to the forward solution coordinate frame
```

Time-frequency beamforming based on DICS

```
# Setting frequency bins as in Dalal et al. 2008
freq_bins = [(4, 12), (12, 30), (30, 55), (65, 300)] # Hz
win_lengths = [0.3, 0.2, 0.15, 0.1] # s
# Then set FFTs length for each frequency range.
# Should be a power of 2 to be faster.
n_ffts = [256, 128, 128, 128]
# Subtract evoked response prior to computation?
subtract_evoked = False
# Calculating noise cross-spectral density from empty room noise for each
# frequency bin and the corresponding time window length. To calculate noise
# from the baseline period in the data, change epochs_noise to epochs
noise_csds = []
for freq_bin, win_length, n_fft in zip(freq_bins, win_lengths, n_ffts):
noise_csd = csd_fourier(epochs_noise, fmin=freq_bin[0], fmax=freq_bin[1],
tmin=-win_length, tmax=0, n_fft=n_fft)
noise_csds.append(noise_csd.sum())
# Computing DICS solutions for time-frequency windows in a label in source
# space for faster computation, use label=None for full solution
stcs = tf_dics(epochs, forward, noise_csds, tmin, tmax, tstep, win_lengths,
freq_bins=freq_bins, subtract_evoked=subtract_evoked,
n_ffts=n_ffts, reg=0.05, label=label, inversion='matrix')
# Plotting source spectrogram for source with maximum activity
# Note that tmin and tmax are set to display a time range that is smaller than
# the one for which beamforming estimates were calculated. This ensures that
# all time bins shown are a result of smoothing across an identical number of
# time windows.
plot_source_spectrogram(stcs, freq_bins, tmin=tmin_plot, tmax=tmax_plot,
source_index=None, colorbar=True)
```

Out:

```
Computing cross-spectral density from epochs...
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[done]
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[done]
Computing time-frequency DICS beamformer for time window -500 to -200 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window -450 to -150 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window -400 to -100 ms, in frequency range 4 to 12 Hz
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Computing time-frequency DICS beamformer for time window -99 to 200 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window -49 to 250 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 0 to 300 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 50 to 350 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 100 to 400 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 150 to 450 ms, in frequency range 4 to 12 Hz
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Computing time-frequency DICS beamformer for time window 250 to 550 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 300 to 600 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 350 to 650 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 400 to 700 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window 450 to 750 ms, in frequency range 4 to 12 Hz
Computing time-frequency DICS beamformer for time window -500 to -300 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -450 to -250 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -400 to -200 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -350 to -149 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -300 to -99 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -250 to -49 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -199 to 0 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -149 to 50 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -99 to 100 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -49 to 150 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window 0 to 200 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window 50 to 250 ms, in frequency range 12 to 30 Hz
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Computing time-frequency DICS beamformer for time window 150 to 350 ms, in frequency range 12 to 30 Hz
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Computing time-frequency DICS beamformer for time window 250 to 450 ms, in frequency range 12 to 30 Hz
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Computing time-frequency DICS beamformer for time window 350 to 550 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window 400 to 600 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window 450 to 650 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window 500 to 700 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window 550 to 750 ms, in frequency range 12 to 30 Hz
Computing time-frequency DICS beamformer for time window -500 to -350 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window -450 to -300 ms, in frequency range 30 to 55 Hz
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Computing time-frequency DICS beamformer for time window 300 to 450 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window 350 to 500 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window 400 to 550 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window 450 to 600 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window 500 to 650 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window 550 to 700 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window 600 to 750 ms, in frequency range 30 to 55 Hz
Computing time-frequency DICS beamformer for time window -500 to -400 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -450 to -350 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -400 to -300 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -350 to -249 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -300 to -199 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -250 to -150 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -199 to -99 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -149 to -49 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -99 to 0 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window -49 to 50 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 0 to 100 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 50 to 150 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 100 to 200 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 150 to 250 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 200 to 300 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 250 to 350 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 300 to 400 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 350 to 450 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 400 to 500 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 450 to 550 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 500 to 600 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 550 to 650 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 600 to 700 ms, in frequency range 65 to 300 Hz
Computing time-frequency DICS beamformer for time window 650 to 750 ms, in frequency range 65 to 300 Hz
```

**Total running time of the script:** ( 0 minutes 25.041 seconds)

**Estimated memory usage:** 443 MB