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

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

doi:10.21105/joss.01896

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

J Open Source Softw. 2019;4(44):1896. doi: 10.21105/joss.01896. Epub 2019 Dec 18.

Authors

Stefan Appelhoff¹, Matthew Sanderson², Teon L Brooks³, Marijn van Vliet⁴, Romain Quentin⁵, Chris Holdgraf⁶, Maximilien Chaumon⁷, Ezequiel Mikulan⁸, Kambiz Tavabi⁹, Richard Höchenberger¹⁰, Dominik Welke¹¹, Clemens Brunner¹², Alexander P Rockhill¹³, Eric Larson⁹, Alexandre Gramfort¹⁴, Mainak Jas¹⁵

Affiliations

¹ Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany.
² Department of Cognitive Sciences, Macquarie University, Sydney, Australia.
³ Mozilla.
⁴ Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland.
⁵ Human Cortical Physiology and Neurorehabilitation Section, NINDS, NIH, Bethesda, Maryland 20892.
⁶ UC Berkeley, Project Jupyter.
⁷ Institut du cerveau et de la moelle épinière (ICM), Paris, France.
⁸ Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
⁹ Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA.
¹⁰ Institute of Neuroscience and Medicine (INM-3), Research Center Jülich, Germany.
¹¹ Max-Planck-Institute for Empirical Aesthetics, Frankfurt a.M., Germany.
¹² Institute of Psychology, University of Graz, Austria.
¹³ University of Oregon, Eugene OR, USA.
¹⁴ Université Paris-Saclay, Inria, CEA, Palaiseau, France.
¹⁵ Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA.

Abstract

The 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.

Abstract

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