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%matplotlib inline

Compute source space connectivity and visualize it using a circular graph

This example computes the all-to-all connectivity between 68 regions in source space based on dSPM inverse solutions and a FreeSurfer cortical parcellation. The connectivity is visualized using a circular graph which is ordered based on the locations of the regions in the axial plane.



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# Authors: Martin Luessi <mluessi@nmr.mgh.harvard.edu>
#          Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#          Nicolas P. Rougier (graph code borrowed from his matplotlib gallery)
#
# License: BSD (3-clause)

import numpy as np
import matplotlib.pyplot as plt

import mne
from mne.datasets import sample
from mne.minimum_norm import apply_inverse_epochs, read_inverse_operator
from mne.connectivity import spectral_connectivity
from mne.viz import circular_layout, plot_connectivity_circle

print(__doc__)

Load our data

First we'll load the data we'll use in connectivity estimation. We'll use the sample MEG data provided with MNE.



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data_path = sample.data_path()
subjects_dir = data_path + '/subjects'
fname_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif'
fname_raw = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
fname_event = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'

# Load data
inverse_operator = read_inverse_operator(fname_inv)
raw = mne.io.read_raw_fif(fname_raw)
events = mne.read_events(fname_event)

# Add a bad channel
raw.info['bads'] += ['MEG 2443']

# Pick MEG channels
picks = mne.pick_types(raw.info, meg=True, eeg=False, stim=False, eog=True,
                       exclude='bads')

# Define epochs for left-auditory condition
event_id, tmin, tmax = 1, -0.2, 0.5
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), reject=dict(mag=4e-12, grad=4000e-13,
                                                    eog=150e-6))

Compute inverse solutions and their connectivity

Next, we need to compute the inverse solution for this data. This will return the sources / source activity that we'll use in computing connectivity. We'll compute the connectivity in the alpha band of these sources. We can specify particular frequencies to include in the connectivity with the fmin and fmax flags. Notice from the status messages how mne-python:

reads an epoch from the raw file
applies SSP and baseline correction
computes the inverse to obtain a source estimate
averages the source estimate to obtain a time series for each label
includes the label time series in the connectivity computation
moves to the next epoch.

This behaviour is because we are using generators. Since we only need to operate on the data one epoch at a time, using a generator allows us to compute connectivity in a computationally efficient manner where the amount of memory (RAM) needed is independent from the number of epochs.



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# Compute inverse solution and for each epoch. By using "return_generator=True"
# stcs will be a generator object instead of a list.
snr = 1.0  # use lower SNR for single epochs
lambda2 = 1.0 / snr ** 2
method = "dSPM"  # use dSPM method (could also be MNE or sLORETA)
stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, method,
                            pick_ori="normal", return_generator=True)

# Get labels for FreeSurfer 'aparc' cortical parcellation with 34 labels/hemi
labels = mne.read_labels_from_annot('sample', parc='aparc',
                                    subjects_dir=subjects_dir)
label_colors = [label.color for label in labels]

# Average the source estimates within each label using sign-flips to reduce
# signal cancellations, also here we return a generator
src = inverse_operator['src']
label_ts = mne.extract_label_time_course(stcs, labels, src, mode='mean_flip',
                                         return_generator=True)

fmin = 8.
fmax = 13.
sfreq = raw.info['sfreq']  # the sampling frequency
con_methods = ['pli', 'wpli2_debiased']
con, freqs, times, n_epochs, n_tapers = spectral_connectivity(
    label_ts, method=con_methods, mode='multitaper', sfreq=sfreq, fmin=fmin,
    fmax=fmax, faverage=True, mt_adaptive=True, n_jobs=1)

# con is a 3D array, get the connectivity for the first (and only) freq. band
# for each method
con_res = dict()
for method, c in zip(con_methods, con):
    con_res[method] = c[:, :, 0]

Make a connectivity plot

Now, we visualize this connectivity using a circular graph layout.



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# First, we reorder the labels based on their location in the left hemi
label_names = [label.name for label in labels]

lh_labels = [name for name in label_names if name.endswith('lh')]

# Get the y-location of the label
label_ypos = list()
for name in lh_labels:
    idx = label_names.index(name)
    ypos = np.mean(labels[idx].pos[:, 1])
    label_ypos.append(ypos)

# Reorder the labels based on their location
lh_labels = [label for (yp, label) in sorted(zip(label_ypos, lh_labels))]

# For the right hemi
rh_labels = [label[:-2] + 'rh' for label in lh_labels]

# Save the plot order and create a circular layout
node_order = list()
node_order.extend(lh_labels[::-1])  # reverse the order
node_order.extend(rh_labels)

node_angles = circular_layout(label_names, node_order, start_pos=90,
                              group_boundaries=[0, len(label_names) / 2])

# Plot the graph using node colors from the FreeSurfer parcellation. We only
# show the 300 strongest connections.
plot_connectivity_circle(con_res['pli'], label_names, n_lines=300,
                         node_angles=node_angles, node_colors=label_colors,
                         title='All-to-All Connectivity left-Auditory '
                               'Condition (PLI)')

Make two connectivity plots in the same figure

We can also assign these connectivity plots to axes in a figure. Below we'll show the connectivity plot using two different connectivity methods.



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fig = plt.figure(num=None, figsize=(8, 4), facecolor='black')
no_names = [''] * len(label_names)
for ii, method in enumerate(con_methods):
    plot_connectivity_circle(con_res[method], no_names, n_lines=300,
                             node_angles=node_angles, node_colors=label_colors,
                             title=method, padding=0, fontsize_colorbar=6,
                             fig=fig, subplot=(1, 2, ii + 1))

plt.show()

Save the figure (optional)

By default matplotlib does not save using the facecolor, even though this was set when the figure was generated. If not set via savefig, the labels, title, and legend will be cut off from the output png file.



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# fname_fig = data_path + '/MEG/sample/plot_inverse_connect.png'
# fig.savefig(fname_fig, facecolor='black')