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2 samples permutation test on source data with spatio-temporal clustering¶
Tests if the source space data are significantly different between 2 groups of subjects (simulated here using one subject’s data). The multiple comparisons problem is addressed with a cluster-level permutation test across space and time.
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# License: BSD-3-Clause
import os.path as op
import numpy as np
from scipy import stats as stats
import mne
from mne import spatial_src_adjacency
from mne.stats import spatio_temporal_cluster_test, summarize_clusters_stc
from mne.datasets import sample
print(__doc__)
Set parameters¶
data_path = sample.data_path()
stc_fname = data_path + '/MEG/sample/sample_audvis-meg-lh.stc'
subjects_dir = data_path + '/subjects'
src_fname = subjects_dir + '/fsaverage/bem/fsaverage-ico-5-src.fif'
# Load stc to in common cortical space (fsaverage)
stc = mne.read_source_estimate(stc_fname)
stc.resample(50, npad='auto')
# Read the source space we are morphing to
src = mne.read_source_spaces(src_fname)
fsave_vertices = [s['vertno'] for s in src]
morph = mne.compute_source_morph(stc, 'sample', 'fsaverage',
spacing=fsave_vertices, smooth=20,
subjects_dir=subjects_dir)
stc = morph.apply(stc)
n_vertices_fsave, n_times = stc.data.shape
tstep = stc.tstep * 1000 # convert to milliseconds
n_subjects1, n_subjects2 = 6, 7
print('Simulating data for %d and %d subjects.' % (n_subjects1, n_subjects2))
# Let's make sure our results replicate, so set the seed.
np.random.seed(0)
X1 = np.random.randn(n_vertices_fsave, n_times, n_subjects1) * 10
X2 = np.random.randn(n_vertices_fsave, n_times, n_subjects2) * 10
X1[:, :, :] += stc.data[:, :, np.newaxis]
# make the activity bigger for the second set of subjects
X2[:, :, :] += 3 * stc.data[:, :, np.newaxis]
# We want to compare the overall activity levels for each subject
X1 = np.abs(X1) # only magnitude
X2 = np.abs(X2) # only magnitude
Out:
Reading a source space...
[done]
Reading a source space...
[done]
2 source spaces read
Simulating data for 6 and 7 subjects.
Compute statistic¶
To use an algorithm optimized for spatio-temporal clustering, we just pass the spatial adjacency matrix (instead of spatio-temporal)
print('Computing adjacency.')
adjacency = spatial_src_adjacency(src)
# Note that X needs to be a list of multi-dimensional array of shape
# samples (subjects_k) x time x space, so we permute dimensions
X1 = np.transpose(X1, [2, 1, 0])
X2 = np.transpose(X2, [2, 1, 0])
X = [X1, X2]
# Now let's actually do the clustering. This can take a long time...
# Here we set the threshold quite high to reduce computation,
# and use a very low number of permutations for the same reason.
n_permutations = 50
p_threshold = 0.001
f_threshold = stats.distributions.f.ppf(1. - p_threshold / 2.,
n_subjects1 - 1, n_subjects2 - 1)
print('Clustering.')
T_obs, clusters, cluster_p_values, H0 = clu =\
spatio_temporal_cluster_test(
X, adjacency=adjacency, n_jobs=1, n_permutations=n_permutations,
threshold=f_threshold, buffer_size=None)
# Now select the clusters that are sig. at p < 0.05 (note that this value
# is multiple-comparisons corrected).
good_cluster_inds = np.where(cluster_p_values < 0.05)[0]
Out:
Computing adjacency.
-- number of adjacent vertices : 20484
Clustering.
stat_fun(H1): min=0.000000 max=303.632172
Running initial clustering
Found 361 clusters
Permuting 49 times...
0%| | : 0/49 [00:00<?, ?it/s]
2%|2 | : 1/49 [00:00<00:01, 29.27it/s]
4%|4 | : 2/49 [00:00<00:01, 29.39it/s]
8%|8 | : 4/49 [00:00<00:01, 39.79it/s]
10%|# | : 5/49 [00:00<00:01, 37.05it/s]
14%|#4 | : 7/49 [00:00<00:01, 41.91it/s]
16%|#6 | : 8/49 [00:00<00:01, 39.58it/s]
20%|## | : 10/49 [00:00<00:00, 42.82it/s]
22%|##2 | : 11/49 [00:00<00:00, 40.86it/s]
27%|##6 | : 13/49 [00:00<00:00, 43.33it/s]
29%|##8 | : 14/49 [00:00<00:00, 41.62it/s]
33%|###2 | : 16/49 [00:00<00:00, 43.64it/s]
35%|###4 | : 17/49 [00:00<00:00, 42.12it/s]
39%|###8 | : 19/49 [00:00<00:00, 43.87it/s]
41%|#### | : 20/49 [00:00<00:00, 42.48it/s]
45%|####4 | : 22/49 [00:00<00:00, 44.02it/s]
47%|####6 | : 23/49 [00:00<00:00, 42.74it/s]
51%|#####1 | : 25/49 [00:00<00:00, 44.14it/s]
53%|#####3 | : 26/49 [00:00<00:00, 42.93it/s]
57%|#####7 | : 28/49 [00:00<00:00, 44.23it/s]
59%|#####9 | : 29/49 [00:00<00:00, 43.09it/s]
63%|######3 | : 31/49 [00:00<00:00, 44.31it/s]
65%|######5 | : 32/49 [00:00<00:00, 43.22it/s]
69%|######9 | : 34/49 [00:00<00:00, 44.36it/s]
71%|#######1 | : 35/49 [00:00<00:00, 43.32it/s]
76%|#######5 | : 37/49 [00:00<00:00, 44.41it/s]
78%|#######7 | : 38/49 [00:00<00:00, 43.41it/s]
82%|########1 | : 40/49 [00:00<00:00, 44.45it/s]
84%|########3 | : 41/49 [00:00<00:00, 43.48it/s]
88%|########7 | : 43/49 [00:00<00:00, 44.48it/s]
90%|########9 | : 44/49 [00:01<00:00, 43.53it/s]
94%|#########3| : 46/49 [00:01<00:00, 44.51it/s]
96%|#########5| : 47/49 [00:01<00:00, 43.58it/s]
100%|##########| : 49/49 [00:01<00:00, 45.00it/s]
100%|##########| : 49/49 [00:01<00:00, 44.09it/s]
Computing cluster p-values
Done.
Visualize the clusters¶
print('Visualizing clusters.')
# Now let's build a convenient representation of each cluster, where each
# cluster becomes a "time point" in the SourceEstimate
fsave_vertices = [np.arange(10242), np.arange(10242)]
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
subjects_dir = op.join(data_path, 'subjects')
# blue blobs are for condition A != condition B
brain = stc_all_cluster_vis.plot('fsaverage', hemi='both',
views='lateral', subjects_dir=subjects_dir,
time_label='temporal extent (ms)',
clim=dict(kind='value', lims=[0, 1, 40]))
Out:
Visualizing clusters.
Total running time of the script: ( 0 minutes 15.421 seconds)
Estimated memory usage: 70 MB