Release Notes for cog_ieeg - v.0.1.0

We are excited to announce the release of the cog_ieeg repository, a comprehensive toolbox accompanying our Scientific Data paper submitted in Nature. This toolbox is designed to simplify the process of downloading, preprocessing, analyzing, and visualizing our iEEG dataset collected as part of the (COGITATE project)[https://www.arc-cogitate.com/]. Below are the key features and components included in this release:

Key features

1. Data utilities:

• Download Functions (cog_ieeg.xnat_utilities): Easily download the iEEG dataset from the designated database.
• Data processing functions (cog_ieeg.processing): Contains various functions to process iEEG data (notch filtering, removing bad channels based on annotations, computing high gamma...)
• Functions to handle channels localization (cog_ieeg.localization): Contains various functions to handle iEEG channels localization on brain surface
• Vizualization (cog_ieeg.vizualization): Generate detailed plots of the iEEG signals and electrodes localizations data for visualization and interpretation.

2. Pipelines

• Preprocessing Pipeline (cog_ieeg.pipelines.Preprocessing): Automate the preprocessing of iEEG data using this ready-to-use pipeline.
• Onset Responsiveness Pipeline (cog_ieeg.pipelines.OnsetResponsiveness): Execute the onset responsiveness analysis pipeline.
• Decoding Pipeline (cog_ieeg.pipelines.Decoding): Implement decoding analysis with a dedicated pipeline.

3. Jupyter Notebooks

• Showcase Notebook: A general notebook demonstrating how to use our dataset, along with educational content on iEEG data analysis.
• Subject-Specific Report Notebook: Automatically generate HTML reports for individual subjects, providing detailed insights into their data. This notebook can be run on each subject independently.

Note: The Jupyter notebooks are located in the root directory of the repository, separate from the core package.

Installation

The toolbox can be installed via pip:

pip install git+https://github.com/Cogitate-consortium/iEEG-data-release.git@main#egg=cog_ieeg

Note: To use the notebooks, you will need to download the repository itself!

Acknowledgments

This work was supported by the Templeton World Charity Foundation (TWCF0389) and the Max Planck Society. We would also like to thank all members of the cogitate consortium for their support and invaluable input in developing this toolbox.

Authors:

• Alex Lepauvre
• Simon Henin
• Katarina Bendtz
• Praveen Sripad
• Niccolò Bonacchi
• Gabriel Kreiman
• Lucia Melloni