MNE-RSA

This is a Python package for performing representational similarity analysis (RSA) using MNE-Python data structures. The main use-case is to perform RSA using a “searchlight” approach through time and/or a volumetric or surface source space.

Read more on RSA in the paper that introduced the technique:

Nikolaus Kriegeskorte, Marieke Mur and Peter Bandettini (2008). Representational similarity analysis - connecting the branches of systems neuroscience. Frontiers in Systems Neuroscience, 2(4). https://doi.org/10.3389/neuro.06.004.2008

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Use cases

This is what the package can do for you:

• Compute RDMs on arbitrary data

• Compute RDMs in a searchlight across:

  • vertices/voxels and samples (source level)
  • sensors and samples (sensor level)
  • vertices/voxels only (source level)
  • sensors only (sensor level)
  • samples only (source and sensor level)

• Use cross-validated distance metrics when computing RDMs

• And of course: compute RSA between RDMs

Supported metrics for comparing RDMs:

• Spearman correlation (the default)
• Pearson correlation
• Kendall’s Tau-A
• Linear regression (when comparing multiple RDMs at once)
• Partial correlation (when comparing multiple RDMs at once)

Installation

The package can be installed either through PIP: pip install mne-rsa
or through conda using the conda-forge channel: conda install -c conda-forge mne-rsa

Example usage

Basic example on the EEG “kiloword” data:

import mne
import mne_rsa
data_path = mne.datasets.kiloword.data_path(verbose=True)
epochs = mne.read_epochs(data_path / "kword_metadata-epo.fif")
# Create model RDMs based on each stimulus property
columns = epochs.metadata.columns[1:]  # Skip the first column: WORD
model_rdms = [mne_rsa.compute_rdm(epochs.metadata[col], metric="euclidean") for col in columns]
# Perform RSA in a sliding window across time
rsa_results = mne_rsa.rsa_epochs(epochs, model_rdms, temporal_radius=0.01)
# Plot the result
mne.viz.plot_compare_evokeds({column: result for column, result in zip(columns, rsa_results)},
                            picks="rsa", legend="lower center", title="RSA result")

Documentation

For a detailed guide on RSA analyis from start to finish on an example dataset, see the tutorials.

For quick guides on how to do specific things, see the examples.

Finally, there is the API reference documentation.

Integration with other packages

The main purpose of this package is to perform RSA analysis on MEG data. Hence, integration functions with MNE-Python are provided. However, there is also some integration with nipy for fMRI that should well in a nilearn setup.

Support

This free software comes without any form of official support. However, if you think you have encountered a bug or have a particularly great idea for improvements, please open an issue on Github. For questions and help with your analysis, you are welcome to post on the MNE forum.

Contributing

Development of the package happens on Github. Everyone is welcome to raise issues or contribute pull requests.

Here is how to install the additional required packages for developing MNE-RSA and set up the package in development mode:

git clone [email protected]:mne-tools/mne-rsa.git
cd mne-rsa
pip install -r requirements-dev.txt
pip install -e .

To run the test suite, execute pytest in the main mne-rsa folder.
To build the documentation, execute make html in the mne-rsa/doc folder (or on Windows: sphinx-build . _build/html).

Citation

If you end up using this package for the data analysis that is part of a scientific article, please cite:

Marijn van Vliet, Takao Shimizu, Stefan Appelhoff, Yuan-Fang Zhao, & Richard Höchenberger. (2024). mne-tools/mne-rsa: Version 0.9.1 (0.9.1). Zenodo. https://doi.org/10.5281/zenodo.11258133