MVAR connectivity and example

.travis.yml

@@ -53,6 +53,7 @@ install:
     - source ${MNE_ROOT}/bin/mne_setup_sh;
     - conda install --yes --quiet $ENSURE_PACKAGES pandas$PANDAS scikit-learn$SKLEARN patsy h5py pillow;
     - pip install -q joblib nibabel;
+    - pip install -q scot==0.2.1
     - if [ "${PYTHON}" == "3.5" ]; then
         conda install --yes --quiet $ENSURE_PACKAGES ipython;
       else

examples/connectivity/plot_mne_inverse_label_connectivity.py

@@ -0,0 +1,164 @@
+"""
+=========================================================================
+Compute source space connectivity and visualize it using a circular graph
+=========================================================================
+
+This example computes connectivity between 68 regions in source space based on
+dSPM inverse solutions and a FreeSurfer cortical parcellation. All-to-all
+functional and effective connectivity measures are obtained from two different
+methods: non-parametric spectral estimates and multivariate autoregressive
+(MVAR) models. The connectivity is visualized using a circular graph which is
+ordered based on the locations of the regions.
+
+MVAR connectivity is computed with the Source Connectivity Toolbox (SCoT), see
+http://scot-dev.github.io/scot-doc/index.html for details.
+"""
+# Authors: Martin Luessi <[email protected]>
+#          Alexandre Gramfort <[email protected]>
+#          Martin Billinger <[email protected]>
+#          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_sandbox.connectivity import mvar_connectivity
+from mne.viz import circular_layout
+from mne_sandbox.viz import (plot_connectivity_circle,
+                             plot_connectivity_inoutcircles)
+from scot.connectivity_statistics import significance_fdr
+
+print(__doc__)
+
+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 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. We do not return a generator, because we want to use
+# the estimates repeatedly.
+src = inverse_operator['src']
+label_ts = mne.extract_label_time_course(stcs, labels, src, mode='mean_flip',
+                                         return_generator=False)
+
+# First, compute connectivity from spectral estimates in the alpha band.
+fmin = 8.
+fmax = 13.
+sfreq = raw.info['sfreq']  # the sampling frequency
+con_methods = ['wpli2_debiased', 'coh']
+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_spec = dict()
+for method, c in zip(con_methods, con):
+    con_spec[method] = c[:, :, 0]
+
+# Second, compute connectivity from multivariate autoregressive models.
+mvar_methods = ['PDC', 'COH']
+con, freqs, order, p_vals = mvar_connectivity(label_ts, mvar_methods,
+                                              sfreq=sfreq, fmin=fmin,
+                                              fmax=fmax, ridge=10,
+                                              n_surrogates=100, n_jobs=1)
+
+# Get connectivity for the first frequency band. Set connectivity to 0 if not
+# significant, while compensating for multiple testing by controlling the false
+# discovery rate.
+con_mvar = dict()
+for method, c, p in zip(mvar_methods, con, p_vals):
+    con_mvar[method] = c[:, :, 0] * significance_fdr(p[:, :, 0], 0.01)
+
+# Now, we visualize the connectivity using a circular graph layout
+
+# 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_spec['wpli2_debiased'], label_names, n_lines=300,
+                         node_angles=node_angles, node_colors=label_colors,
+                         title='All-to-All Connectivity left-Auditory '
+                               'Condition (WPLI^2, debiased)', show=False)
+plt.savefig('circle.png', facecolor='black')
+
+# Compare coherence from both estimation methods
+fig = plt.figure(num=None, figsize=(8, 4), facecolor='black')
+for ii, (con, method) in enumerate(zip([con_spec['coh'], con_mvar['COH']],
+                                       ['Spectral', 'MVAR'])):
+    plot_connectivity_circle(con, label_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), plot_names=False,
+                             show=False)
+plt.suptitle('All-to-all coherence', color='white', fontsize=14)
+
+# Show effective (directed) connectivity for one node
+plot_connectivity_inoutcircles(con_mvar['PDC'], 'superiortemporal-lh',
+                               label_names, node_angles=node_angles, padding=0,
+                               node_colors=label_colors, plot_names=False,
+                               title='Effective connectivity (PDC)', show=False)
+
+plt.show()

mne_sandbox/connectivity/__init__.py

@@ -0,0 +1,4 @@
+""" Connectivity Analysis Tools
+"""
+
+from .mvar import mvar_connectivity