Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Angela Renton; Thuy Thanh Dao; Tom Johnstone; Oren Civier; Ryan P. Sullivan; David White; Paris Lyons; Benjamin Slade; David F. Abbott; Toluwani Joan Amos; Saskia Bollmann; Andy Botting; Megan E. J. Campbell; Jeryn Chang; Thomas Close; Monika Dörig; Korbinian Eckstein; Gary F. Egan; Stefanie Evas; Guillaume Flandin; Kelly Garner; Marta Isabel Garrido; Satrajit Ghosh; Martin Grignard; Yaroslav O. Halchenko; Anthony John Hannan; Anibal Sólon Heinsfeld; Laurentius Huber; Matthew Edward Hughes; Jakub Kaczmarzyk

doi:10.1038/s41592-023-02145-x

NeuroscienceNature MethodsJan 8, 2024

Peer-reviewed journal article

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Angela Renton iD, Thuy Thanh Dao iD, Tom Johnstone iD, Oren Civier iD, Ryan P. Sullivan iD, David White iD, Paris Lyons, Benjamin Slade iD, David F. Abbott iD, Toluwani Joan Amos iD, Saskia Bollmann iD, Andy Botting, Megan E. J. Campbell iD, Jeryn Chang iD, Thomas Close iD, Monika Dörig iD, Korbinian Eckstein iD, Gary F. Egan iD, Stefanie Evas iD, Guillaume Flandin iD, Kelly Garner iD, Marta Isabel Garrido iD, Satrajit Ghosh iD, Martin Grignard iD, Yaroslav O. Halchenko iD, , Steffen Bollmann iD

Abstract

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

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