Note
Click here to download the full example code
Visualising statistical significance thresholds on EEG data¶
MNE-Python provides a range of tools for statistical hypothesis testing and the visualisation of the results. Here, we show a few options for exploratory and confirmatory tests - e.g., targeted t-tests, cluster-based permutation approaches (here with Threshold-Free Cluster Enhancement); and how to visualise the results.
The underlying data comes from 1; we contrast long vs. short words. TFCE is described in 2.
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import ttest_ind
import mne
from mne.channels import find_ch_adjacency, make_1020_channel_selections
from mne.stats import spatio_temporal_cluster_test
np.random.seed(0)
# Load the data
path = mne.datasets.kiloword.data_path() + '/kword_metadata-epo.fif'
epochs = mne.read_epochs(path)
name = "NumberOfLetters"
# Split up the data by the median length in letters via the attached metadata
median_value = str(epochs.metadata[name].median())
long_words = epochs[name + " > " + median_value]
short_words = epochs[name + " < " + median_value]
Out:
Reading /home/circleci/mne_data/MNE-kiloword-data/kword_metadata-epo.fif ...
Isotrak not found
Found the data of interest:
t = -100.00 ... 920.00 ms
0 CTF compensation matrices available
Adding metadata with 8 columns
Replacing existing metadata with 8 columns
960 matching events found
No baseline correction applied
0 projection items activated
If we have a specific point in space and time we wish to test, it can be
convenient to convert the data into Pandas Dataframe format. In this case,
the mne.Epochs object has a convenient
mne.Epochs.to_data_frame() method, which returns a dataframe.
This dataframe can then be queried for specific time windows and sensors.
The extracted data can be submitted to standard statistical tests. Here,
we conduct t-tests on the difference between long and short words.
time_windows = ((.2, .25), (.35, .45))
elecs = ["Fz", "Cz", "Pz"]
index = ['condition', 'epoch', 'time']
# display the EEG data in Pandas format (first 5 rows)
print(epochs.to_data_frame(index=index)[elecs].head())
report = "{elec}, time: {tmin}-{tmax} s; t({df})={t_val:.3f}, p={p:.3f}"
print("\nTargeted statistical test results:")
for (tmin, tmax) in time_windows:
long_df = long_words.copy().crop(tmin, tmax).to_data_frame(index=index)
short_df = short_words.copy().crop(tmin, tmax).to_data_frame(index=index)
for elec in elecs:
# extract data
A = long_df[elec].groupby("condition").mean()
B = short_df[elec].groupby("condition").mean()
# conduct t test
t, p = ttest_ind(A, B)
# display results
format_dict = dict(elec=elec, tmin=tmin, tmax=tmax,
df=len(epochs.events) - 2, t_val=t, p=p)
print(report.format(**format_dict))
Out:
channel Fz ... Pz
condition epoch time ...
film 0 -100 0.421970 ... 0.398182
-96 0.453939 ... 0.222424
-92 0.465606 ... 0.018485
-88 0.468182 ... -0.173485
-84 0.483485 ... -0.312121
[5 rows x 3 columns]
Targeted statistical test results:
Fz, time: 0.2-0.25 s; t(958)=-0.572, p=0.568
Cz, time: 0.2-0.25 s; t(958)=-2.836, p=0.005
Pz, time: 0.2-0.25 s; t(958)=-3.938, p=0.000
Fz, time: 0.35-0.45 s; t(958)=5.192, p=0.000
Cz, time: 0.35-0.45 s; t(958)=5.555, p=0.000
Pz, time: 0.35-0.45 s; t(958)=6.353, p=0.000
Absent specific hypotheses, we can also conduct an exploratory mass-univariate analysis at all sensors and time points. This requires correcting for multiple tests. MNE offers various methods for this; amongst them, cluster-based permutation methods allow deriving power from the spatio-temoral correlation structure of the data. Here, we use TFCE.
# Calculate adjacency matrix between sensors from their locations
adjacency, _ = find_ch_adjacency(epochs.info, "eeg")
# Extract data: transpose because the cluster test requires channels to be last
# In this case, inference is done over items. In the same manner, we could
# also conduct the test over, e.g., subjects.
X = [long_words.get_data().transpose(0, 2, 1),
short_words.get_data().transpose(0, 2, 1)]
tfce = dict(start=.2, step=.2)
# Calculate statistical thresholds
t_obs, clusters, cluster_pv, h0 = spatio_temporal_cluster_test(
X, tfce, adjacency=adjacency,
n_permutations=100) # a more standard number would be 1000+
significant_points = cluster_pv.reshape(t_obs.shape).T < .05
print(str(significant_points.sum()) + " points selected by TFCE ...")
Out:
Could not find a adjacency matrix for the data. Computing adjacency based on Delaunay triangulations.
-- number of adjacent vertices : 29
stat_fun(H1): min=0.000000 max=81.298503
Running initial clustering
Using 406 thresholds from 0.20 to 81.20 for TFCE computation (h_power=2.00, e_power=0.50)
Found 7424 clusters
Permuting 99 times...
0%| | : 0/99 [00:00<?, ?it/s]
1%|1 | : 1/99 [00:00<00:52, 1.85it/s]
2%|2 | : 2/99 [00:00<00:38, 2.49it/s]
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Computing cluster p-values
Done.
1433 points selected by TFCE ...
The results of these mass univariate analyses can be visualised by plotting
mne.Evoked objects as images (via mne.Evoked.plot_image)
and masking points for significance.
Here, we group channels by Regions of Interest to facilitate localising
effects on the head.
# We need an evoked object to plot the image to be masked
evoked = mne.combine_evoked([long_words.average(), short_words.average()],
weights=[1, -1]) # calculate difference wave
time_unit = dict(time_unit="s")
evoked.plot_joint(title="Long vs. short words", ts_args=time_unit,
topomap_args=time_unit) # show difference wave
# Create ROIs by checking channel labels
selections = make_1020_channel_selections(evoked.info, midline="12z")
# Visualize the results
fig, axes = plt.subplots(nrows=3, figsize=(8, 8))
axes = {sel: ax for sel, ax in zip(selections, axes.ravel())}
evoked.plot_image(axes=axes, group_by=selections, colorbar=False, show=False,
mask=significant_points, show_names="all", titles=None,
**time_unit)
plt.colorbar(axes["Left"].images[-1], ax=list(axes.values()), shrink=.3,
label="µV")
plt.show()
Out:
No projector specified for this dataset. Please consider the method self.add_proj.
References¶
- 1
Stéphane Dufau, Jonathan Grainger, Katherine J. Midgley, and Phillip J. Holcomb. A thousand words are worth a picture: snapshots of printed-word processing in an event-related potential megastudy. Psychological Science, 26(12):1887–1897, 2015. doi:10.1177/0956797615603934.
- 2
Stephen M. Smith and Thomas E. Nichols. Threshold-free cluster enhancement: addressing problems of smoothing, threshold dependence and localisation in cluster inference. NeuroImage, 44(1):83–98, 2009. doi:10.1016/j.neuroimage.2008.03.061.
Total running time of the script: ( 0 minutes 52.670 seconds)
Estimated memory usage: 171 MB