MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis.

Stefan Appelhoff,Richard Höchenberger,Maximilien Chaumon,Matthew Sanderson,Alexander Rockhill,Chris Holdgraf,Mainak Jas,Eric Larson,Alexandre Gramfort,Kambiz Tavabi,Teon Brooks,Marijn Van Vliet,Clemens Brunner,Romain Quentin,Dominik Welke,Ezequiel Mikulan

doi:10.21105/joss.01896

Abstract

SummaryThe development of the Brain Imaging Data Structure (BIDS; Gorgolewski et al., 2016) gave the neuroscientific community a standard to organize and share data. BIDS prescribes file naming conventions and a folder structure to store data in a set of already existing file formats. Next to rules about organization of the data itself, BIDS provides standardized templates to store associated metadata in the form of Javascript Object Notation (JSON) and tab separated value (TSV) files. It thus facilitates data sharing, eases metadata querying, and enables automatic data analysis pipelines. BIDS is a rich system to curate, aggregate, and annotate neuroimaging databases.

Highlights

The development of the Brain Imaging Data Structure (BIDS; Gorgolewski et al, 2016) gave the neuroscientific community a standard to organize and share data
While BIDS was originally intended for magnetic resonance imaging (MRI) data, it has extensions for other data modalities including: magnetoencephalography (MEG; Niso et al, 2018), electroencephalography (EEG; Pernet et al, 2019), and intracranial encephalography
Within the Python ecosystem, MNE-Python (Gramfort et al, 2013) is a major software package for electrophysiology data analysis, and extending its functionality to support BIDS would be a great benefit for its growing user base

Summary

Introduction

The development of the Brain Imaging Data Structure (BIDS; Gorgolewski et al, 2016) gave the neuroscientific community a standard to organize and share data. To rules about organization of the data itself, BIDS provides standardized templates to store associated metadata in the form of Javascript Object Notation (JSON) and tab separated value (TSV) files. It facilitates data sharing, eases metadata querying, and enables automatic data analysis pipelines.

Results

Conclusion