Spatiotemporal permutation F-test on full sensor data¶

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'
event_id = {'Aud/L': 1, 'Aud/R': 2, 'Vis/L': 3, 'Vis/R': 4}
tmin = -0.2
tmax = 0.5

# Setup for reading the raw data
raw = mne.io.read_raw_fif(raw_fname, preload=True)
raw.filter(1, 30, fir_design='firwin')
events = mne.read_events(event_fname)

picks = mne.pick_types(raw.info, meg='mag', eog=True)

reject = dict(mag=4e-12, eog=150e-6)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=None, reject=reject, preload=True)

epochs.drop_channels(['EOG 061'])
epochs.equalize_event_counts(event_id)

X = [epochs[k].get_data() for k in event_id]  # as 3D matrix
X = [np.transpose(x, (0, 2, 1)) for x in X]  # transpose for clustering

connectivity, ch_names = find_ch_connectivity(epochs.info, ch_type='mag')

print(type(connectivity))  # it's a sparse matrix!

plt.imshow(connectivity.toarray(), cmap='gray', origin='lower',
           interpolation='nearest')
plt.xlabel('{} Magnetometers'.format(len(ch_names)))
plt.ylabel('{} Magnetometers'.format(len(ch_names)))
plt.title('Between-sensor adjacency')

# set cluster threshold
threshold = 50.0  # very high, but the test is quite sensitive on this data
# set family-wise p-value
p_accept = 0.01

cluster_stats = spatio_temporal_cluster_test(X, n_permutations=1000,
                                             threshold=threshold, tail=1,
                                             n_jobs=1,
                                             connectivity=connectivity)

T_obs, clusters, p_values, _ = cluster_stats
good_cluster_inds = np.where(p_values < p_accept)[0]

# configure variables for visualization
colors = {"Aud": "crimson", "Vis": 'steelblue'}
linestyles = {"L": '-', "R": '--'}

# get sensor positions via layout
pos = mne.find_layout(epochs.info).pos

# organize data for plotting
evokeds = {cond: epochs[cond].average() for cond in event_id}

# loop over clusters
for i_clu, clu_idx in enumerate(good_cluster_inds):
    # unpack cluster information, get unique indices
    time_inds, space_inds = np.squeeze(clusters[clu_idx])
    ch_inds = np.unique(space_inds)
    time_inds = np.unique(time_inds)

    # get topography for F stat
    f_map = T_obs[time_inds, ...].mean(axis=0)

    # get signals at the sensors contributing to the cluster
    sig_times = epochs.times[time_inds]

    # create spatial mask
    mask = np.zeros((f_map.shape[0], 1), dtype=bool)
    mask[ch_inds, :] = True

    # initialize figure
    fig, ax_topo = plt.subplots(1, 1, figsize=(10, 3))

    # plot average test statistic and mark significant sensors
    image, _ = plot_topomap(f_map, pos, mask=mask, axes=ax_topo, cmap='Reds',
                            vmin=np.min, vmax=np.max, show=False)

    # create additional axes (for ERF and colorbar)
    divider = make_axes_locatable(ax_topo)

    # add axes for colorbar
    ax_colorbar = divider.append_axes('right', size='5%', pad=0.05)
    plt.colorbar(image, cax=ax_colorbar)
    ax_topo.set_xlabel(
        'Averaged F-map ({:0.3f} - {:0.3f} s)'.format(*sig_times[[0, -1]]))

    # add new axis for time courses and plot time courses
    ax_signals = divider.append_axes('right', size='300%', pad=1.2)
    title = 'Cluster #{0}, {1} sensor'.format(i_clu + 1, len(ch_inds))
    if len(ch_inds) > 1:
        title += "s (mean)"
    plot_compare_evokeds(evokeds, title=title, picks=ch_inds, axes=ax_signals,
                         colors=colors, linestyles=linestyles, show=False,
                         split_legend=True, truncate_yaxis='max_ticks')

    # plot temporal cluster extent
    ymin, ymax = ax_signals.get_ylim()
    ax_signals.fill_betweenx((ymin, ymax), sig_times[0], sig_times[-1],
                             color='orange', alpha=0.3)

    # clean up viz
    mne.viz.tight_layout(fig=fig)
    fig.subplots_adjust(bottom=.05)
    plt.show()