Note
Click here to download the full example code
This example demonstrates how to perform representational similarity analysis (RSA) on EEG data, using a searchlight approach.
In the searchlight approach, representational similarity is computed between the model and searchlight “patches”. A patch is defined by a seed point (e.g. sensor Pz) and everything within the given radius (e.g. all sensors within 4 cm. of Pz). Patches are created for all possible seed points (e.g. all sensors), so you can think of it as a “searchlight” that moves from seed point to seed point and everything that is in the spotlight is used in the computation.
The radius of a searchlight can be defined in space, in time, or both. In this example, our searchlight will have a spatial radius of 4.5 cm. and a temporal radius of 50 ms.
The dataset will be the kiloword dataset [1]: approximately 1,000 words were presented to 75 participants in a go/no-go lexical decision task while event-related potentials (ERPs) were recorded.
# sphinx_gallery_thumbnail_number=2
# Import required packages
import mne
import mne_rsa
MNE-Python contains a build-in data loader for the kiloword dataset. We use it here to read it as 960 epochs. Each epoch represents the brain response to a single word, averaged across all the participants. For this example, we speed up the computation, at a cost of temporal precision, by downsampling the data from the original 250 Hz. to 100 Hz.
data_path = mne.datasets.kiloword.data_path(verbose=True)
epochs = mne.read_epochs(data_path / 'kword_metadata-epo.fif')
epochs = epochs.resample(100)
# Drop some
epochs.drop([0, 10, 20, 100], reason='BAD')
dsms = mne_rsa.dsm_epochs(
epochs,
spatial_radius=None,
temporal_radius=0.05,
dropped_as_nan=True,
)
dsm = next(dsms)
Reading C:\Users\wmvan\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
960 matching events found
No baseline correction applied
0 projection items activated
Dropped 4 epochs: 0, 10, 20, 100
Creating temporal searchlight patches
The kiloword datas was erroneously stored with sensor locations given in centimeters instead of meters. We will fix it now. For your own data, the sensor locations are likely properly stored in meters, so you can skip this step.
for ch in epochs.info['chs']:
ch['loc'] /= 100
Total running time of the script: ( 0 minutes 4.044 seconds)