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

Nature Methods (2024)Cite this article

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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.

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Fig. 1: The Neurodesk platform.
Fig. 2: Inter-computer differences in an fMRI processing pipeline.

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Data availability

The data that support the findings of the case study are available from the ICBM database (https://www.loni.usc.edu/). There are restrictions that apply to the availability of these data, which were used under approved permission for the current study, and thus are not publicly available but are available from ICBM upon request. Source data are provided with this paper.

Code availability

The code for this project is publicly available on GitHub, across multiple repositories under the https://github.com/NeuroDesk/ organization. It has also been archived on Zenodo at https://doi.org/10.5281/zenodo.8053090. The code is licensed under the MIT License.

All stages of development, from the initial conception as a hackathon project, through to the most current iteration of Neurodesk, with up-to-date community-built Neurocontainer recipes, are documented publicly across the project’s GitHub repository and the platform’s website; which contains descriptions of how code is organized on the GitHub repository, and how to contribute to the project (https://www.neurodesk.org/).

Any issues can be logged at https://github.com/orgs/NeuroDesk/discussions/. Contributions can be made by any community member with a GitHub account and the eagerness to create pull requests.

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Acknowledgements

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.

Author information

Author notes

  1. These authors contributed equally: Angela I. Renton, Thuy T. Dao.

  2. These authors jointly supervised this work: Aswin Narayanan, Steffen Bollmann.

Authors and Affiliations

  1. The University of Queensland, Queensland Brain Institute, St Lucia, Brisbane, Queensland, Australia

    Angela I. Renton & Jason B. Mattingley

  2. The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia

    Angela I. Renton, Thuy T. Dao, Saskia Bollmann, Korbinian Eckstein, Kexin Lou, Fernanda L. Ribeiro, Thomas B. Shaw, Ashley W. Stewart, Xincheng Ye & Steffen Bollmann

  3. Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia

    Tom Johnstone, Oren Civier, David J. White, Paris Lyons, Benjamin M. Slade & Matthew E. Hughes

  4. The University of Sydney, School of Biomedical Engineering, Sydney, New South Wales, Australia

    Ryan P. Sullivan & Thomas G. Close

  5. The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia

    David F. Abbott & Anthony J. Hannan

  6. School of Life Science and Technology, University of Electronic Science and Technology, Chengdu, China

    Toluwani J. Amos

  7. Australian Research Data Commons (ARDC), Sydney, New South Wales, Australia

    Andy Botting & Jo Morris

  8. School of Psychological Sciences, University of Newcastle, Newcastle, New South Wales, Australia

    Megan E. J. Campbell

  9. Hunter Medical Research Institute Imaging Centre, Newcastle, New South Wales, Australia

    Megan E. J. Campbell

  10. The University of Queensland, School of Biomedical Sciences, St Lucia, Brisbane, Queensland, Australia

    Jeryn Chang

  11. Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, University of Zurich, Zurich, Switzerland

    Monika Dörig & Michael L. Meier

  12. The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia

    Gary F. Egan & Nigel C. Rogasch

  13. Monash Biomedical Imaging, Monash University, Melbourne, Victoria, Australia

    Gary F. Egan

  14. School of Psychology, University of Adelaide, Adelaide, South Australia, Australia

    Stefanie Evas

  15. Human Health, Health & Biosecurity, CSIRO, Adelaide, South Australia, Australia

    Stefanie Evas

  16. Wellcome Centre for Human Neuroimaging, University College London, London, UK

    Guillaume Flandin

  17. School of Psychology, University of New South Wales, Sydney, New South Wales, Australia

    Kelly G. Garner

  18. The University of Queensland, School of Psychology, St Lucia, Brisbane, Queensland, Australia

    Kelly G. Garner & Jason B. Mattingley

  19. Melbourne School of Psychological Sciences, he University of Melbourne, Melbourne, Victoria, Australia

    Marta I. Garrido

  20. Graeme Clark Institute for Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia

    Marta I. Garrido

  21. McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA

    Satrajit S. Ghosh

  22. Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA

    Satrajit S. Ghosh

  23. GIGA CRC In-Vivo Imaging, University of Liège, Liège, Belgium

    Martin Grignard

  24. Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA

    Yaroslav O. Halchenko

  25. Department of Psychology, Center for Perceptual Systems, Institute for Neuroscience, Center For Learning and Memory, The University of Texas at Austin, Austin, TX, USA

    Anibal S. Heinsfeld & Franco Pestilli

  26. National Institute of Mental Health (NIMH), National Institutes Health, Bethesda, MD, USA

    Laurentius Huber

  27. Department of Biomedical Informatics, Stony Brook University, New York, NY, USA

    Jakub R. Kaczmarzyk

  28. Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, New York, NY, USA

    Jakub R. Kaczmarzyk

  29. BRAIN-TO Lab, Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada

    Lars Kasper

  30. Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland

    Lars Kasper

  31. Department of Data Science and AI, Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia

    Levin Kuhlmann

  32. Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China

    Kexin Lou

  33. Grupo Neuropsicología y Conducta (GRUNECO), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia

    Yorguin-Jose Mantilla-Ramos

  34. School of Computer Science, The University of Auckland, Auckland, New Zealand

    Akshaiy Narayanan

  35. Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA

    Aina Puce

  36. Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia

    Nigel C. Rogasch

  37. Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia

    Nigel C. Rogasch

  38. McCausland Center for Brain Imaging, Department of Psychology, University of South Carolina, Columbia, SC, USA

    Chris Rorden

  39. School of Psychology, University of Wollongong, Wollongong, New South Wales, Australia

    Mark M. Schira

  40. The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia

    Thomas B. Shaw, Aswin Narayanan & Steffen Bollmann

  41. Department of Neurology, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia

    Thomas B. Shaw

  42. Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia

    Paul F. Sowman & Judy D. Zhu

  43. Department of Neuroscience, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia

    Gershon Spitz

  44. Monash-Epworth Rehabilitation Research Centre, Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia

    Gershon Spitz

  45. ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, Queensland, Australia

    Ashley W. Stewart & Steffen Bollmann

  46. Queensland Digital Health Centre, The University of Queensland, Brisbane, Queensland, Australia

    Steffen Bollmann

Authors
  1. Angela I. Renton
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  2. Thuy T. Dao
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  3. Tom Johnstone
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  4. Oren Civier
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Contributions

Conceptualization: S.B., A.N., O.C., T.J., D.W., A.R., T.S., R.S., T.C., A.H., G.E., M.G., A.P., F.P., M.G., L.K., G.S., D.A., M.C., N.R., J.R.K., S.G., P.F.S., S.B. and J.B.M. Software: S.B., A.N., T.S., O.C., T.J., D.W., A.N., T.D., A.S., M.G., L.K., J.D.Z., K.E., S.E., X.Y., F.R., J.C., K.L., J.M., R.H., Y.-J.M.-R., J.R.K., A.B., C.R., Y.O.H. and A.S.H. Validation: S.B., A.N., T.J.A., A.R., T.S., O.C., D.W., K.G., T.D., A.S., L.K., J.D.Z., K.E., G.F., M.G., S.E., X.Y., M.S., F.R., J.C., J.K., K.L., L.H., R.S., T.C., M.H., L.K., G.S., D.A., M.C., N.R., M.G., A.P., M.D. and M.L.M. Formal analysis: T.D. Conceptualization of formal analysis: S.B., T.D., A.R., F.R. and T.S. Writing—initial outline: A.R., O.C., P.L. and S.B. Writing—original draft: A.R. Writing—review and editing: all authors. Visualization: A.R. Supervision: S.B., T.J. and A.R. Project administration: S.B., A.N., P.L., T.J., O.C. and B.S. Funding acquisition: S.B., A.N., O.C., T.J., D.W. and R.S.

Corresponding authors

Correspondence to Angela I. Renton or Steffen Bollmann.

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Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Taiga Abe, Agah Karakuzu, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Nina Vogt, in collaboration with the Nature Methods team. Peer reviewer reports are available.

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Extended data

Extended Data Table 1 Tools currently available in Neurodesk
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Supplementary information

Supplementary Information

Supplementary Notes, Figs. 1–4 and Tables 1 and 2.

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Peer Review File

Source data

Source Data Fig. 2

Statistical source data. This zipped folder contains .nii files—a universally accepted file format for storing the type of neuroimaging data plotted in the figure.

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Renton, A.I., Dao, T.T., Johnstone, T. et al. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nat Methods (2024). https://doi.org/10.1038/s41592-023-02145-x

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