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

Angela I. Renton, Thuy T. Dao, Tom Johnstone, Oren Civier, Ryan P. Sullivan, David J. White, Paris Lyons, Benjamin M. Slade, David F. Abbott, Toluwani J. Amos, Saskia Bollmann, Andy Botting, Megan E.J. Campbell, Jeryn Chang, Thomas G. Close, Monika Dörig, Korbinian Eckstein, Gary F. Egan, Stefanie Evas, Guillaume FlandinKelly G. Garner, Marta I. Garrido, Satrajit S. Ghosh, Martin Grignard, Yaroslav O. Halchenko, Anthony J. Hannan, Anibal S. Heinsfeld, Laurentius Huber, Matthew E. Hughes, Jakub R. Kaczmarzyk, Lars Kasper, Levin Kuhlmann, Kexin Lou, Yorguin Jose Mantilla-Ramos, Jason B. Mattingley, Michael L. Meier, Jo Morris, Akshaiy Narayanan, Franco Pestilli, Aina Puce, Fernanda L. Ribeiro, Nigel C. Rogasch, Chris Rorden, Mark M. Schira, Thomas B. Shaw, Paul F. Sowman, Gershon Spitz, Ashley W. Stewart, Xincheng Ye, Judy D. Zhu, Aswin Narayanan, Steffen Bollmann

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform (https://www.neurodesk.org/) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.

Original languageEnglish
Pages (from-to)804-808
Number of pages5
JournalNature Methods
Volume21
Issue number5
Early online date8 Jan 2024
DOIs
StatePublished - May 2024
Externally publishedYes

Bibliographical note

Publisher Copyright:
© The Author(s), under exclusive licence to Springer Nature America, Inc. 2024.

Funding

The ARDC invested in Neurodesk’s development through the Australian Electrophysiology Data Analytics Platform project (S.B., A.N., O.C., T.J. and R.S.). We thank Oracle for Research for providing Oracle Cloud credits and related cloud resources to support this project (S.B.) The University of Queensland funded the project via the Knowledge Exchange & Translation Fund and the UQ AI Collaboratory (S.B.). S.B., F.L.R. and A.W.S. acknowledge funding through an ARC Linkage grant (LP200301393). S.B. and A.W.S. acknowledge funding through the Australian Research Council Training Centre for Innovation in Biomedical Imaging Technology (IC170100035). This research was supported by use of the Nectar Research Cloud, a collaborative Australian research platform supported by the National Collaborative Research Infrastructure Strategy-funded ARDC. We acknowledge the facilities and scientific and technical assistance of the National Imaging Facility, a National Collaborative Research Infrastructure Strategy capability. A National Institutes of Health grant (P41EB019936) partially supported J.R.K. and S.S.G. Data collection and sharing for this project was provided by the International Consortium for Brain Mapping (ICBM; Principal Investigator: J. Mazziotta). ICBM funding was provided by the National Institute of Biomedical Imaging and BioEngineering. ICBM data are disseminated by the Laboratory of Neuro Imaging at the University of Southern California. We thank I. C. D. Lenton, E. Cooper-Williams and Y. ‘Sam’ Peng for contributions to the first NeuroDesk precursor ‘Dicom2Cloud’ and the reviewers for the constructive feedback. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

FundersFunder number
Australian Research Council Training Centre for Innovation in Biomedical Imaging TechnologyIC170100035
International Consortium for Brain Mapping
Knowledge Exchange & Translation Fund
UQ AI Collaboratory
National Institutes of HealthP41EB019936
National Institute of Biomedical Imaging and Bioengineering
Australian Research CouncilLP200301393
University of Queensland

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