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%matplotlib inline
This example computes the all-to-all connectivity between 75 regions in a mixed 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.
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# Author: Annalisa Pascarella <a.pascarella@iac.cnr.it>
#
# License: BSD (3-clause)
import os.path as op
import numpy as np
import mne
import matplotlib.pyplot as plt
from mne.datasets import sample
from mne import setup_volume_source_space, setup_source_space
from mne import make_forward_solution
from mne.io import read_raw_fif
from mne.minimum_norm import make_inverse_operator, apply_inverse_epochs
from mne.connectivity import spectral_connectivity
from mne.viz import circular_layout, plot_connectivity_circle
# Set dir
data_path = sample.data_path()
subject = 'sample'
data_dir = op.join(data_path, 'MEG', subject)
subjects_dir = op.join(data_path, 'subjects')
bem_dir = op.join(subjects_dir, subject, 'bem')
# Set file names
fname_aseg = op.join(subjects_dir, subject, 'mri', 'aseg.mgz')
fname_model = op.join(bem_dir, '%s-5120-bem.fif' % subject)
fname_bem = op.join(bem_dir, '%s-5120-bem-sol.fif' % subject)
fname_raw = data_dir + '/sample_audvis_filt-0-40_raw.fif'
fname_trans = data_dir + '/sample_audvis_raw-trans.fif'
fname_cov = data_dir + '/ernoise-cov.fif'
fname_event = data_dir + '/sample_audvis_filt-0-40_raw-eve.fif'
# List of sub structures we are interested in. We select only the
# sub structures we want to include in the source space
labels_vol = ['Left-Amygdala',
'Left-Thalamus-Proper',
'Left-Cerebellum-Cortex',
'Brain-Stem',
'Right-Amygdala',
'Right-Thalamus-Proper',
'Right-Cerebellum-Cortex']
# Setup a surface-based source space
src = setup_source_space(subject, subjects_dir=subjects_dir,
spacing='oct6', add_dist=False)
# Setup a volume source space
# set pos=7.0 for speed issue
vol_src = setup_volume_source_space(subject, mri=fname_aseg,
pos=7.0,
bem=fname_model,
volume_label=labels_vol,
subjects_dir=subjects_dir)
# Generate the mixed source space
src += vol_src
# compute the fwd matrix
fwd = make_forward_solution(fname_raw, fname_trans, src, fname_bem,
mindist=5.0, # ignore sources<=5mm from innerskull
meg=True, eeg=False,
n_jobs=1)
# Load data
raw = read_raw_fif(fname_raw, preload=True)
noise_cov = mne.read_cov(fname_cov)
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 solution and for each epoch
snr = 1.0 # use smaller SNR for raw data
inv_method = 'dSPM'
parc = 'aparc' # the parcellation to use, e.g., 'aparc' 'aparc.a2009s'
lambda2 = 1.0 / snr ** 2
# Compute inverse operator
inverse_operator = make_inverse_operator(raw.info, fwd, noise_cov,
depth=None, fixed=False)
stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, inv_method,
pick_ori=None, return_generator=True)
# Get labels for FreeSurfer 'aparc' cortical parcellation with 34 labels/hemi
labels_parc = mne.read_labels_from_annot(subject, parc=parc,
subjects_dir=subjects_dir)
# Average the source estimates within each label of the cortical parcellation
# and each sub structures contained in the src space
# If mode = 'mean_flip' this option is used only for the cortical label
src = inverse_operator['src']
label_ts = mne.extract_label_time_course(stcs, labels_parc, src,
mode='mean_flip',
allow_empty=True,
return_generator=False)
# We compute the connectivity in the alpha band and plot it using a circular
# graph layout
fmin = 8.
fmax = 13.
sfreq = raw.info['sfreq'] # the sampling frequency
con, freqs, times, n_epochs, n_tapers = spectral_connectivity(
label_ts, method='pli', mode='multitaper', sfreq=sfreq, fmin=fmin,
fmax=fmax, faverage=True, mt_adaptive=True, n_jobs=1)
# We create a list of Label containing also the sub structures
labels_aseg = mne.get_volume_labels_from_src(src, subject, subjects_dir)
labels = labels_parc + labels_aseg
# read colors
node_colors = [label.color for label in labels]
# 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')]
rh_labels = [name for name in label_names if name.endswith('rh')]
# Get the y-location of the label
label_ypos_lh = list()
for name in lh_labels:
idx = label_names.index(name)
ypos = np.mean(labels[idx].pos[:, 1])
label_ypos_lh.append(ypos)
try:
idx = label_names.index('Brain-Stem')
except ValueError:
pass
else:
ypos = np.mean(labels[idx].pos[:, 1])
lh_labels.append('Brain-Stem')
label_ypos_lh.append(ypos)
# Reorder the labels based on their location
lh_labels = [label for (yp, label) in sorted(zip(label_ypos_lh, lh_labels))]
# For the right hemi
rh_labels = [label[:-2] + 'rh' for label in lh_labels
if label != 'Brain-Stem' and label[:-2] + 'rh' in rh_labels]
# Save the plot order
node_order = list()
node_order = lh_labels[::-1] + 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.
conmat = con[:, :, 0]
fig = plt.figure(num=None, figsize=(8, 8), facecolor='black')
plot_connectivity_circle(conmat, label_names, n_lines=300,
node_angles=node_angles, node_colors=node_colors,
title='All-to-All Connectivity left-Auditory '
'Condition (PLI)', fig=fig, interactive=False)
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# fname_fig = data_path + '/MEG/sample/plot_mixed_connect.png'
# plt.savefig(fname_fig, facecolor='black')