Note
Go to the end to download the full example code.
Determine the significance of connectivity estimates against baseline connectivity#
This example demonstrates how surrogate data can be generated to assess whether connectivity estimates are significantly greater than baseline.
# Author: Thomas S. Binns <t.s.binns@outlook.com>
# License: BSD (3-clause)
# sphinx_gallery_thumbnail_number = 3
import matplotlib.pyplot as plt
import mne
import numpy as np
from mne.datasets import somato
from mne_connectivity import make_surrogate_data, spectral_connectivity_epochs
Background#
When performing connectivity analyses, we often want to know whether the results we observe reflect genuine interactions between signals. We can assess this by performing statistical tests between our connectivity estimates and a ‘baseline’ level of connectivity. However, due to factors such as background noise and sample size-dependent biases (see e.g. [1]), it is often not appropriate to treat 0 as this baseline. Therefore, we need a way to estimate the baseline level of connectivity.
One approach is to manipulate the original data in such a way that the covariance structure is destroyed, creating surrogate data. Connectivity estimates from the original and surrogate data can then be compared to determine whether the original data contains significant interactions.
Such surrogate data can be easily generated in MNE using the
make_surrogate_data() function, which shuffles epoched data
independently across channels [2] (see the Notes section of
the function for more information). In this example, we will demonstrate how surrogate
data can be created, and how you can use this to assess the statistical significance
of your connectivity estimates.
Loading the data#
We start by loading from the Somatosensory dataset, MEG data showing event-related activity in response to somatosensory stimuli. We construct epochs around these events in the time window [-1.5, 1.0] seconds.
# Load data
data_path = somato.data_path()
raw_fname = data_path / "sub-01" / "meg" / "sub-01_task-somato_meg.fif"
raw = mne.io.read_raw_fif(raw_fname)
events = mne.find_events(raw, stim_channel="STI 014")
# Pre-processing
raw.pick("grad").load_data() # focus on gradiometers
raw.filter(1, 35)
raw, events = raw.resample(sfreq=100, events=events) # reduce compute time
# Construct epochs around events
epochs = mne.Epochs(
raw, events, event_id=1, tmin=-1.5, tmax=1.0, baseline=(-0.5, 0), preload=True
)
epochs = epochs[:30] # select a subset of epochs to speed up computation
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Download complete in 19s (582.2 MB)
Opening raw data file /home/circleci/mne_data/MNE-somato-data/sub-01/meg/sub-01_task-somato_meg.fif...
Range : 237600 ... 506999 = 791.189 ... 1688.266 secs
Ready.
111 events found on stim channel STI 014
Event IDs: [1]
Reading 0 ... 269399 = 0.000 ... 897.077 secs...
Filtering raw data in 1 contiguous segment
Setting up band-pass filter from 1 - 35 Hz
FIR filter parameters
---------------------
Designing a one-pass, zero-phase, non-causal bandpass filter:
- Windowed time-domain design (firwin) method
- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
- Lower passband edge: 1.00
- Lower transition bandwidth: 1.00 Hz (-6 dB cutoff frequency: 0.50 Hz)
- Upper passband edge: 35.00 Hz
- Upper transition bandwidth: 8.75 Hz (-6 dB cutoff frequency: 39.38 Hz)
- Filter length: 993 samples (3.307 s)
[Parallel(n_jobs=1)]: Done 17 tasks | elapsed: 0.1s
[Parallel(n_jobs=1)]: Done 71 tasks | elapsed: 0.5s
[Parallel(n_jobs=1)]: Done 161 tasks | elapsed: 1.2s
Not setting metadata
111 matching events found
Applying baseline correction (mode: mean)
0 projection items activated
Using data from preloaded Raw for 111 events and 251 original time points ...
0 bad epochs dropped
Assessing connectivity in non-evoked data#
We will first demonstrate how connectivity can be assessed from non-evoked data. In
this example, we use data from the pre-trial period of [-1.5, -0.5] seconds. We
compute Fourier coefficients of the data using the compute_psd()
method with output="complex" (note that this requires mne >= 1.8).
Next, we pass these coefficients to
spectral_connectivity_epochs() to compute connectivity using
the imaginary part of coherency (imcoh). Our indices specify that connectivity
should be computed between all pairs of channels.
# Compute Fourier coefficients for pre-trial data
fmin, fmax = 3, 23
pretrial_coeffs = epochs.compute_psd(
fmin=fmin, fmax=fmax, tmin=None, tmax=-0.5, output="complex"
)
freqs = pretrial_coeffs.freqs
# Compute connectivity for pre-trial data
indices = np.tril_indices(epochs.info["nchan"], k=-1) # all-to-all connectivity
pretrial_con = spectral_connectivity_epochs(
pretrial_coeffs, method="imcoh", indices=indices
)
Using multitaper spectrum estimation with 7 DPSS windows
Connectivity computation...
frequencies: 4.0Hz..22.8Hz (20 points)
computing connectivity for 20706 connections
the following metrics will be computed: Imaginary Coherence
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[Connectivity computation done]
Next, we generate the surrogate data by passing the Fourier coefficients into the
make_surrogate_data() function. To get a reliable estimate of
the baseline connectivity, we perform this shuffling procedure
\(\text{n}_{\text{shuffle}}\) times, producing \(\text{n}_{\text{shuffle}}\)
surrogate datasets. We can then iterate over these shuffles and compute the
connectivity for each one.
# Generate surrogate data
n_shuffles = 100 # recommended is >= 1,000; limited here to reduce compute time
pretrial_surrogates = make_surrogate_data(
pretrial_coeffs, n_shuffles=n_shuffles, rng_seed=44
)
# Compute connectivity for surrogate data
surrogate_con = []
for shuffle_i, surrogate in enumerate(pretrial_surrogates, 1):
print(f"Computing connectivity for shuffle {shuffle_i} of {n_shuffles}")
surrogate_con.append(
spectral_connectivity_epochs(
surrogate, method="imcoh", indices=indices, verbose=False
)
)
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We can plot the all-to-all connectivity of the pre-trial data against the surrogate data, averaged over all shuffles. This shows a strong degree of coupling in the alpha band (~8-12 Hz), with weaker coupling in the lower range of the beta band (~13-20 Hz). A simple visual inspection shows that connectivity in the alpha and beta bands are above the baseline level of connectivity estimated from the surrogate data. However, we need to confirm this statistically.
# Plot pre-trial vs. surrogate connectivity
fig, ax = plt.subplots(1, 1)
ax.plot(
freqs,
np.abs([surrogate.get_data() for surrogate in surrogate_con]).mean(axis=(0, 1)),
linestyle="--",
label="Surrogate",
)
ax.plot(freqs, np.abs(pretrial_con.get_data()).mean(axis=0), label="Original")
ax.set_xlabel("Frequency (Hz)")
ax.set_ylabel("Connectivity (A.U.)")
ax.set_title("All-to-all connectivity | Pre-trial ")
ax.legend()
<matplotlib.legend.Legend object at 0x7f0018912860>
Assessing the statistical significance of our connectivity estimates can be done with the following simple procedure [2]
\(p=\LARGE{\frac{\Sigma_{s=1}^Sc_s}{S}}\) ,
\(c_s=\{1\text{ if }\text{Con}\leq\text{Con}_{\text{s}}\text{ },\text{ }0 \text{ if otherwise }\) ,
where: \(p\) is our p-value; \(s\) is a given shuffle iteration of \(S\) total shuffles; and \(c\) is a binary indicator of whether the true connectivity, \(\text{Con}\), is greater than the surrogate connectivity, \(\text{Con}_{\text{s}}\), for a given shuffle.
Note that for connectivity methods which produce negative scores (e.g., imaginary part of coherency, time-reversed Granger causality, etc…), you should take the absolute values before testing. Similar adjustments should be made for methods that produce scores centred around non-zero values (e.g., 0.5 for directed phase lag index).
Below, we determine the statistical significance of connectivity in the lower beta band using an alpha of 0.05. Naturally, any tests involving multiple connections, frequencies, and/or times should be corrected for multiple comparisons. Here however, we average over all connections and frequencies.
The test confirms our visual inspection, showing that connectivity in the lower beta band is significantly above the baseline level of connectivity, which we can take as evidence of genuine interactions in this frequency band.
# Find indices of lower beta frequencies
beta_freqs = np.where((freqs >= 13) & (freqs <= 20))[0]
# Compute lower beta connectivity for pre-trial data (average connections and freqs)
beta_con_pretrial = np.abs(pretrial_con.get_data()[:, beta_freqs]).mean(axis=(0, 1))
# Compute lower beta connectivity for surrogate data (average connections and freqs)
beta_con_surrogate = np.abs(
[surrogate.get_data()[:, beta_freqs] for surrogate in surrogate_con]
).mean(axis=(1, 2))
# Compute p-value for pre-trial lower beta coupling
alpha = 0.05
p_val = np.sum(beta_con_pretrial <= beta_con_surrogate) / n_shuffles
print(f"P < {alpha}") if p_val < alpha else print(f"P > {alpha}")
P < 0.05
Assessing connectivity in evoked data#
When generating surrogate data, it is important to distinguish non-evoked data (e.g., resting-state, pre/inter-trial data) from evoked data (where a stimulus is presented or an action performed at a set time during each epoch). Critically, evoked data contains a temporal structure that is consistent across epochs, and thus shuffling epochs across channels will fail to adequately disrupt the covariance structure.
Any connectivity estimates will therefore overestimate the baseline connectivity in
your data, increasing the likelihood of type II errors (see the Notes section of
make_surrogate_data() for more information, and see the
section Generating surrogate connectivity from inappropriate data for a demonstration).
In cases where you want to assess connectivity in evoked data, you can use surrogates generated from non-evoked data (of the same subject). Here we do just that, comparing connectivity estimates from the pre-trial surrogates to the evoked, post-stimulus response ([0, 1] second).
Again, there is pronounced alpha coupling (stronger than in the pre-trial data) and weaker beta coupling, both of which appear to be above the baseline level of connectivity.
# Compute Fourier coefficients for post-stimulus data
poststim_coeffs = epochs.compute_psd(
fmin=fmin, fmax=fmax, tmin=0, tmax=None, output="complex"
)
# Compute connectivity for post-stimulus data
poststim_con = spectral_connectivity_epochs(
poststim_coeffs, method="imcoh", indices=indices
)
# Plot post-stimulus vs. (pre-trial) surrogate connectivity
fig, ax = plt.subplots(1, 1)
ax.plot(
freqs,
np.abs([surrogate.get_data() for surrogate in surrogate_con]).mean(axis=(0, 1)),
linestyle="--",
label="Surrogate",
)
ax.plot(freqs, np.abs(poststim_con.get_data()).mean(axis=0), label="Original")
ax.set_xlabel("Frequency (Hz)")
ax.set_ylabel("Connectivity (A.U.)")
ax.set_title("All-to-all connectivity | Post-stimulus")
ax.legend()
Using multitaper spectrum estimation with 7 DPSS windows
Connectivity computation...
frequencies: 4.0Hz..22.8Hz (20 points)
computing connectivity for 20706 connections
the following metrics will be computed: Imaginary Coherence
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[Connectivity computation done]
<matplotlib.legend.Legend object at 0x7f0034f096c0>
This is also confirmed by statistical testing, with connectivity in the lower beta band being significantly above the baseline level of connectivity. Thus, using surrogate connectivity estimates from non-evoked data provides a reliable baseline for assessing connectivity in evoked data.
# Compute lower beta connectivity for post-stimulus data (average connections and freqs)
beta_con_poststim = np.abs(poststim_con.get_data()[:, beta_freqs]).mean(axis=(0, 1))
# Compute p-value for post-stimulus lower beta coupling
p_val = np.sum(beta_con_poststim <= beta_con_surrogate) / n_shuffles
print(f"P < {alpha}") if p_val < alpha else print(f"P > {alpha}")
P < 0.05
Generating surrogate connectivity from inappropriate data#
We discussed above how surrogates generated from evoked data risk overestimating the degree of baseline connectivity. We demonstrate this below by generating surrogates from the post-stimulus data.
# Generate surrogates from evoked data
poststim_surrogates = make_surrogate_data(
poststim_coeffs, n_shuffles=n_shuffles, rng_seed=44
)
# Compute connectivity for evoked surrogate data
bad_surrogate_con = []
for shuffle_i, surrogate in enumerate(poststim_surrogates, 1):
print(f"Computing connectivity for shuffle {shuffle_i} of {n_shuffles}")
bad_surrogate_con.append(
spectral_connectivity_epochs(
surrogate, method="imcoh", indices=indices, verbose=False
)
)
Computing connectivity for shuffle 1 of 100
Computing connectivity for shuffle 2 of 100
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Plotting the post-stimulus connectivity against the estimates from the non-evoked and evoked surrogate data, we see that the evoked surrogate data greatly overestimates the baseline connectivity in the alpha band.
Although in this case the alpha connectivity was still far above the baseline from the evoked surrogates, this will not always be the case, and you can see how this risks false negative assessments that connectivity is not significantly different from baseline.
# Plot post-stimulus vs. evoked and non-evoked surrogate connectivity
fig, ax = plt.subplots(1, 1)
ax.plot(
freqs,
np.abs([surrogate.get_data() for surrogate in surrogate_con]).mean(axis=(0, 1)),
linestyle="--",
label="Surrogate (pre-stimulus)",
)
ax.plot(
freqs,
np.abs([surrogate.get_data() for surrogate in bad_surrogate_con]).mean(axis=(0, 1)),
color="C3",
linestyle="--",
label="Surrogate (post-stimulus)",
)
ax.plot(
freqs, np.abs(poststim_con.get_data()).mean(axis=0), color="C1", label="Original"
)
ax.set_xlabel("Frequency (Hz)")
ax.set_ylabel("Connectivity (A.U.)")
ax.set_title("All-to-all connectivity | Post-stimulus")
ax.legend()
<matplotlib.legend.Legend object at 0x7f008cf7f3a0>
Assessing connectivity on a group-level#
While our focus here has been on assessing the significance of connectivity on a single recording-level, we may also want to determine whether group-level connectivity estimates are significantly different from baseline. For this, we can generate surrogates and estimate connectivity alongside the original signals for each piece of data.
There are multiple ways to assess the statistical significance. For example, we can compute p-values for each piece of data using the approach above and combine them for the nested data (e.g., across recordings, subjects, etc…) using Stouffer’s method [3].
Alternatively, we could take the average of the surrogate connectivity estimates
across all shuffles for each piece of data and compare them to the original
connectivity estimates in a paired test. The scipy.stats and mne.stats
modules have many such tools for testing this, e.g., scipy.stats.ttest_1samp(),
mne.stats.permutation_t_test(), etc…
Altogether, surrogate connectivity estimates are a powerful tool for assessing the significance of connectivity estimates, both on a single recording- and group-level.
References#
Total running time of the script: (5 minutes 52.807 seconds)