Note

Click here to download the full example code

# Compute all-to-all connectivity in sensor space#

Computes the Phase Lag Index (PLI) between all gradiometers and shows the connectivity in 3D using the helmet geometry. The left visual stimulation data are used which produces strong connectvitiy in the right occipital sensors.

```
# Author: Martin Luessi <mluessi@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import mne
from mne_connectivity import spectral_connectivity_epochs
from mne.datasets import sample
from mne_connectivity.viz import plot_sensors_connectivity
print(__doc__)
```

Set parameters

```
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
# Setup for reading the raw data
raw = mne.io.read_raw_fif(raw_fname)
events = mne.read_events(event_fname)
# Add a bad channel
raw.info['bads'] += ['MEG 2443']
# Pick MEG gradiometers
picks = mne.pick_types(raw.info, meg='grad', eeg=False, stim=False, eog=True,
exclude='bads')
# Create epochs for the visual condition
event_id, tmin, tmax = 3, -0.2, 1.5 # need a long enough epoch for 5 cycles
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6))
# Compute connectivity for band containing the evoked response.
# We exclude the baseline period:
fmin, fmax = 4., 9.
sfreq = raw.info['sfreq'] # the sampling frequency
tmin = 0.0 # exclude the baseline period
epochs.load_data().pick_types(meg='grad') # just keep MEG and no EOG now
con = spectral_connectivity_epochs(
epochs, method='pli', mode='multitaper', sfreq=sfreq, fmin=fmin, fmax=fmax,
faverage=True, tmin=tmin, mt_adaptive=False, n_jobs=1)
# Now, visualize the connectivity in 3D:
plot_sensors_connectivity(
epochs.info,
con.get_data(output='dense')[:, :, 0])
```

Out:

```
/Users/adamli/Documents/mne-connectivity/examples/sensor_connectivity.py:25: DeprecationWarning: data_path functions now return pathlib.Path objects which do not natively support the plus (+) operator, switch to using forward slash (/) instead. Support for plus will be removed in 1.2.
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
/Users/adamli/Documents/mne-connectivity/examples/sensor_connectivity.py:26: DeprecationWarning: data_path functions now return pathlib.Path objects which do not natively support the plus (+) operator, switch to using forward slash (/) instead. Support for plus will be removed in 1.2.
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
Opening raw data file /Users/adamli/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.
Not setting metadata
73 matching events found
Setting baseline interval to [-0.19979521315838786, 0.0] sec
Applying baseline correction (mode: mean)
4 projection items activated
Loading data for 73 events and 256 original time points ...
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
24 bad epochs dropped
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Adding metadata with 3 columns
Connectivity computation...
only using indices for lower-triangular matrix
computing connectivity for 20503 connections
using t=0.000s..1.498s for estimation (226 points)
frequencies: 4.7Hz..8.6Hz (7 points)
connectivity scores will be averaged for each band
Using multitaper spectrum estimation with 7 DPSS windows
the following metrics will be computed: PLI
computing connectivity for epoch 1
computing connectivity for epoch 2
computing connectivity for epoch 3
computing connectivity for epoch 4
computing connectivity for epoch 5
computing connectivity for epoch 6
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computing connectivity for epoch 49
assembling connectivity matrix
[Connectivity computation done]
<mne.viz.backends._pyvista.PyVistaFigure object at 0x7f7ac1013730>
```

**Total running time of the script:** ( 0 minutes 2.041 seconds)