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"""
=====================================================
Spatiotemporal permutation F-test on full sensor data
=====================================================
Tests for differential evoked responses in at least
one condition using a permutation clustering test.
The FieldTrip neighbor templates will be used to determine
the adjacency between sensors. This serves as a spatial prior
to the clustering. Spatiotemporal clusters will then
be visualized using custom matplotlib code.
Caveat for the interpretation of "significant" clusters: see
the `FieldTrip website`_.
"""
# Authors: Denis Engemann <denis.engemann@gmail.com>
# Jona Sassenhagen <jona.sassenhagen@gmail.com>
#
# License: BSD (3-clause)
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from mne.viz import plot_topomap
import mne
from mne.stats import spatio_temporal_cluster_test
from mne.datasets import sample
from mne.channels import find_ch_connectivity
from mne.viz import plot_compare_evokeds
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'
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)
###############################################################################
# Read epochs for the channel of interest
# ---------------------------------------
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
###############################################################################
# Find the FieldTrip neighbor definition to setup sensor connectivity
# -------------------------------------------------------------------
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')
###############################################################################
# Compute permutation statistic
# -----------------------------
#
# How does it work? We use clustering to `bind` together features which are
# similar. Our features are the magnetic fields measured over our sensor
# array at different times. This reduces the multiple comparison problem.
# To compute the actual test-statistic, we first sum all F-values in all
# clusters. We end up with one statistic for each cluster.
# Then we generate a distribution from the data by shuffling our conditions
# between our samples and recomputing our clusters and the test statistics.
# We test for the significance of a given cluster by computing the probability
# of observing a cluster of that size. For more background read:
# Maris/Oostenveld (2007), "Nonparametric statistical testing of EEG- and
# MEG-data" Journal of Neuroscience Methods, Vol. 164, No. 1., pp. 177-190.
# doi:10.1016/j.jneumeth.2007.03.024
# 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, buffer_size=None,
connectivity=connectivity)
T_obs, clusters, p_values, _ = cluster_stats
good_cluster_inds = np.where(p_values < p_accept)[0]
###############################################################################
# Note. The same functions work with source estimate. The only differences
# are the origin of the data, the size, and the connectivity definition.
# It can be used for single trials or for groups of subjects.
#
# Visualize clusters
# ------------------
# 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()
###############################################################################
# Exercises
# ----------
#
# - What is the smallest p-value you can obtain, given the finite number of
# permutations?
# - use an F distribution to compute the threshold by traditional significance
# levels. Hint: take a look at :obj:`scipy.stats.f`
#
# References
# ==========
# .. _fieldtrip website: http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test # noqa
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