"""
.. _tut-cluster-one-sample-spatiotemporal:
=================================================================
Permutation t-test on source data with spatio-temporal clustering
=================================================================
This example tests if the evoked response is significantly different between
two conditions across subjects. Here just for demonstration purposes
we simulate data from multiple subjects using one subject's data.
The multiple comparisons problem is addressed with a cluster-level
permutation test across space and time.
"""
# Authors: Alexandre Gramfort
# Eric Larson
# Stefan Appelhoff
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
# %%
import numpy as np
from numpy.random import randn
from scipy import stats as stats
import mne
from mne.datasets import sample
from mne.epochs import equalize_epoch_counts
from mne.minimum_norm import apply_inverse, read_inverse_operator
from mne.stats import spatio_temporal_cluster_1samp_test, summarize_clusters_stc
# %%
# Set parameters
# --------------
data_path = sample.data_path()
meg_path = data_path / "MEG" / "sample"
raw_fname = meg_path / "sample_audvis_filt-0-40_raw.fif"
event_fname = meg_path / "sample_audvis_filt-0-40_raw-eve.fif"
subjects_dir = data_path / "subjects"
src_fname = subjects_dir / "fsaverage" / "bem" / "fsaverage-ico-5-src.fif"
tmin = -0.2
tmax = 0.3 # Use a lower tmax to reduce multiple comparisons
# Setup for reading the raw data
raw = mne.io.read_raw_fif(raw_fname)
events = mne.read_events(event_fname)
# %%
# Read epochs for all channels, removing a bad one
# ------------------------------------------------
raw.info["bads"] += ["MEG 2443"]
picks = mne.pick_types(raw.info, meg=True, eog=True, exclude="bads")
event_id = 1 # L auditory
reject = dict(grad=1000e-13, mag=4000e-15, eog=150e-6)
epochs1 = mne.Epochs(
raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0),
reject=reject,
preload=True,
)
event_id = 3 # L visual
epochs2 = mne.Epochs(
raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0),
reject=reject,
preload=True,
)
# Equalize trial counts to eliminate bias (which would otherwise be
# introduced by the abs() performed below)
equalize_epoch_counts([epochs1, epochs2])
# %%
# Transform to source space
# -------------------------
fname_inv = meg_path / "sample_audvis-meg-oct-6-meg-inv.fif"
snr = 3.0
lambda2 = 1.0 / snr**2
method = "dSPM" # use dSPM method (could also be MNE, sLORETA, or eLORETA)
inverse_operator = read_inverse_operator(fname_inv)
sample_vertices = [s["vertno"] for s in inverse_operator["src"]]
# Let's average and compute inverse, resampling to speed things up
evoked1 = epochs1.average()
evoked1.resample(50, npad="auto")
condition1 = apply_inverse(evoked1, inverse_operator, lambda2, method)
evoked2 = epochs2.average()
evoked2.resample(50, npad="auto")
condition2 = apply_inverse(evoked2, inverse_operator, lambda2, method)
# Let's only deal with t > 0, cropping to reduce multiple comparisons
condition1.crop(0, None)
condition2.crop(0, None)
tmin = condition1.tmin
tstep = condition1.tstep * 1000 # convert to milliseconds
# %%
# Transform to common cortical space
# ----------------------------------
#
# Normally you would read in estimates across several subjects and morph
# them to the same cortical space (e.g., fsaverage). For example purposes,
# we will simulate this by just having each "subject" have the same
# response (just noisy in source space) here.
#
# .. note::
# Note that for 6 subjects with a two-sided statistical test, the minimum
# significance under a permutation test is only
# ``p = 1/(2 ** 6) = 0.015``, which is large.
n_vertices_sample, n_times = condition1.data.shape
n_subjects = 6
print(f"Simulating data for {n_subjects} subjects.")
# Let's make sure our results replicate, so set the seed.
np.random.seed(0)
X = randn(n_vertices_sample, n_times, n_subjects, 2) * 10
X[:, :, :, 0] += condition1.data[:, :, np.newaxis]
X[:, :, :, 1] += condition2.data[:, :, np.newaxis]
# %%
# It's a good idea to spatially smooth the data, and for visualization
# purposes, let's morph these to fsaverage, which is a grade 5 source space
# with vertices 0:10242 for each hemisphere. Usually you'd have to morph
# each subject's data separately (and you might want to use morph_data
# instead), but here since all estimates are on 'sample' we can use one
# morph matrix for all the heavy lifting.
# Read the source space we are morphing to
src = mne.read_source_spaces(src_fname)
fsave_vertices = [s["vertno"] for s in src]
morph_mat = mne.compute_source_morph(
src=inverse_operator["src"],
subject_to="fsaverage",
spacing=fsave_vertices,
subjects_dir=subjects_dir,
).morph_mat
n_vertices_fsave = morph_mat.shape[0]
# We have to change the shape for the dot() to work properly
X = X.reshape(n_vertices_sample, n_times * n_subjects * 2)
print("Morphing data.")
X = morph_mat.dot(X) # morph_mat is a sparse matrix
X = X.reshape(n_vertices_fsave, n_times, n_subjects, 2)
# %%
# Finally, we want to compare the overall activity levels in each condition,
# the diff is taken along the last axis (condition). The negative sign makes
# it so condition1 > condition2 shows up as "red blobs" (instead of blue).
X = np.abs(X) # only magnitude
X = X[:, :, :, 0] - X[:, :, :, 1] # make paired contrast
# %%
# Find adjacency matrix
# ---------------------
#
# For cluster-based permutation testing, we must define adjacency relations
# that govern which points can become members of the same cluster. While
# these relations are rather obvious for dimensions such as time or frequency
# they require a bit more work for spatial dimension such as channels or
# source vertices.
#
# Here, to use an algorithm optimized for spatio-temporal clustering, we
# just pass the spatial adjacency matrix (instead of spatio-temporal).
# But note that clustering still takes place along the
# temporal dimension and can be
# controlled via the ``max_step`` parameter in
# :func:`mne.stats.spatio_temporal_cluster_1samp_test`.
#
# If we wanted to specify an adjacency matrix for both space and time
# explicitly we would have to use :func:`mne.stats.combine_adjacency`,
# however for the present case, this is not needed.
print("Computing adjacency.")
adjacency = mne.spatial_src_adjacency(src)
# %%
# Compute statistic
# -----------------
# Note that X needs to be a multi-dimensional array of shape
# observations (subjects) × time × space, so we permute dimensions
X = np.transpose(X, [2, 1, 0])
# Here we set a cluster forming threshold based on a p-value for
# the cluster based permutation test.
# We use a two-tailed threshold, the "1 - p_threshold" is needed
# because for two-tailed tests we must specify a positive threshold.
p_threshold = 0.001
df = n_subjects - 1 # degrees of freedom for the test
t_threshold = stats.distributions.t.ppf(1 - p_threshold / 2, df=df)
# Now let's actually do the clustering. This can take a long time...
print("Clustering.")
T_obs, clusters, cluster_p_values, H0 = clu = spatio_temporal_cluster_1samp_test(
X,
adjacency=adjacency,
n_jobs=None,
threshold=t_threshold,
buffer_size=None,
verbose=True,
)
# %%
# Selecting "significant" clusters
# --------------------------------
# After performing the cluster-based permutationt test, you may wish to
# select the observed clusters that can be considered statistically
# significant under the permutation distribution. This can easily be
# done using the code snippet below.
#
# However, it is crucial to be aware that a statistically significant
# observed cluster does not directly translate into statistical
# significance of the channels, time points, frequency bins, etc. that
# form the cluster!
#
# For more information, see the `FieldTrip tutorial `_.
#
# .. include:: ../../links.inc
# Select the clusters that are statistically significant at p < 0.05
good_clusters_idx = np.where(cluster_p_values < 0.05)[0]
good_clusters = [clusters[idx] for idx in good_clusters_idx]
# %%
# Visualize the clusters
# ----------------------
print("Visualizing clusters.")
# Now let's build a convenient representation of our results, where consecutive
# cluster spatial maps are stacked in the time dimension of a SourceEstimate
# object. This way by moving through the time dimension we will be able to see
# subsequent cluster maps.
stc_all_cluster_vis = summarize_clusters_stc(
clu, tstep=tstep, vertices=fsave_vertices, subject="fsaverage"
)
# Let's actually plot the first "time point" in the SourceEstimate, which
# shows all the clusters, weighted by duration.
# blue blobs are for condition A < condition B, red for A > B
brain = stc_all_cluster_vis.plot(
hemi="both",
views="lateral",
subjects_dir=subjects_dir,
time_label="temporal extent (ms)",
size=(800, 800),
smoothing_steps=5,
clim=dict(kind="value", pos_lims=[0, 1, 40]),
)
# We could save this via the following:
# brain.save_image('clusters.png')