Note
Click here to download the full example code
Compute a Dynamic Imaging of Coherent Sources (DICS) [1] filter from single-trial activity to estimate source power across a frequency band.
| [1] | Gross et al. Dynamic imaging of coherent sources: Studying neural interactions in the human brain. PNAS (2001) vol. 98 (2) pp. 694-699 |
# Author: Marijn van Vliet <w.m.vanvliet@gmail.com>
# Roman Goj <roman.goj@gmail.com>
# Denis Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import numpy as np
import mne
from mne.datasets import sample
from mne.time_frequency import csd_morlet
from mne.beamformer import make_dics, apply_dics_csd
print(__doc__)
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_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'
Reading the raw data:
raw = mne.io.read_raw_fif(raw_fname)
raw.info['bads'] = ['MEG 2443'] # 1 bad MEG channel
# Set picks
picks = mne.pick_types(raw.info, meg=True, eeg=False, eog=False,
stim=False, exclude='bads')
# Read epochs
event_id, tmin, tmax = 1, -0.2, 0.5
events = mne.read_events(event_fname)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
picks=picks, baseline=(None, 0), preload=True,
reject=dict(grad=4000e-13, mag=4e-12))
evoked = epochs.average()
# Read forward operator
forward = mne.read_forward_solution(fname_fwd)
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
72 matching events found
Applying baseline correction (mode: mean)
Not setting metadata
Created an SSP operator (subspace dimension = 3)
3 projection items activated
Loading data for 72 events and 421 original time points ...
Rejecting epoch based on MAG : ['MEG 1711']
1 bad epochs dropped
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
Computing the cross-spectral density matrix at 4 evenly spaced frequencies from 6 to 10 Hz. We use a decim value of 20 to speed up the computation in this example at the loss of accuracy.
csd = csd_morlet(epochs, tmin=0, tmax=0.5, decim=20,
frequencies=np.linspace(6, 10, 4))
# Compute DICS spatial filter and estimate source power.
filters = make_dics(epochs.info, forward, csd, reg=0.5)
stc, freqs = apply_dics_csd(csd, filters)
message = 'DICS source power in the 8-12 Hz frequency band'
brain = stc.plot(surface='inflated', hemi='rh', subjects_dir=subjects_dir,
time_label=message)
Out:
Computing cross-spectral density from epochs...
Computing CSD matrix for epoch 1
Computing CSD matrix for epoch 2
Computing CSD matrix for epoch 3
Computing CSD matrix for epoch 4
Computing CSD matrix for epoch 5
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[done]
305 out of 366 channels remain after picking
Computing DICS spatial filters...
computing DICS spatial filter at 6.0Hz (1/4)
computing DICS spatial filter at 7.333333333333333Hz (2/4)
computing DICS spatial filter at 8.666666666666666Hz (3/4)
computing DICS spatial filter at 10.0Hz (4/4)
Computing DICS source power...
applying DICS spatial filter at 6.0Hz (1/4)
applying DICS spatial filter at 7.333333333333333Hz (2/4)
applying DICS spatial filter at 8.666666666666666Hz (3/4)
applying DICS spatial filter at 10.0Hz (4/4)
[done]
Total running time of the script: ( 0 minutes 43.392 seconds)