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; Korbinian Eckstein; Gary F Egan; Stefanie Evas; Guillaume Flandin; Kelly G Garner; Marta I Garrido; Satrajit S Ghosh; Martin Grignard; Anthony J Hannan; Renzo Huber; Jakub R Kaczmarzyk; Lars Kasper; Levin Kuhlmann; Kexin Lou; Yorguin-Jose Mantilla-Ramos; Jason B Mattingley; Jo Morris; Akshaiy Narayanan; Franco Pestilli; Aina Puce; Fernanda L Ribeiro; Nigel C Rogasch; Chris Rorden; Mark Schira; Thomas B Shaw; Paul F Sowman; Gershon Spitz; Ashley Stewart; Xincheng Ye; Judy D Zhu; Matthew E Hughes; Aswin Narayanan; Steffen Bollmann

doi:10.21203/rs.3.rs-2649734/v1

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

Res Sq [Preprint]. 2023 Mar 13:rs.3.rs-2649734. doi: 10.21203/rs.3.rs-2649734/v1.

Authors

Angela I Renton^{1

2}, Thuy T Dao², Tom Johnstone³, Oren Civier³, Ryan P Sullivan⁴, David J White³, Paris Lyons³, Benjamin M Slade³, David F Abbott⁵, Toluwani J Amos⁶, Saskia Bollmann², Andy Botting⁷, Megan E J Campbell^{8

9}, Jeryn Chang¹⁰, Thomas G Close⁴, Korbinian Eckstein², Gary F Egan^{11

12}, Stefanie Evas^{13

14}, Guillaume Flandin¹⁵, Kelly G Garner^{1

16}, Marta I Garrido^{17

18}, Satrajit S Ghosh^{19

20}, Martin Grignard²¹, Anthony J Hannan⁵, Renzo Huber²², Jakub R Kaczmarzyk^{23

24}, Lars Kasper²⁵, Levin Kuhlmann²⁶, Kexin Lou², Yorguin-Jose Mantilla-Ramos²⁷, Jason B Mattingley^{1

16}, Jo Morris⁷, Akshaiy Narayanan²⁸, Franco Pestilli²⁹, Aina Puce³⁰, Fernanda L Ribeiro², Nigel C Rogasch^{31

32

11}, Chris Rorden³³, Mark Schira³⁴, Thomas B Shaw^{2

35

36}, Paul F Sowman³⁷, Gershon Spitz^{38

39}, Ashley Stewart², Xincheng Ye², Judy D Zhu³⁷, Matthew E Hughes³, Aswin Narayanan³⁵, Steffen Bollmann²

Affiliations

¹ The University of Queensland, Queensland Brain Institute, St Lucia 4072, Australia.
² The University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
³ Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
⁴ The University of Sydney, School of Biomedical Engineering, Sydney, Australia.
⁵ The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.
⁶ School of Life Science and Technology, University of Electronic Science and Technology, China.
⁷ Australian Research Data Commons (ARDC), Australia.
⁸ School of Psychological Sciences, University of Newcastle, Australia.
⁹ Hunter Medical Research Institute Imaging Centre, Newcastle, Australia.
¹⁰ The University of Queensland, School of Biomedical Sciences, St Lucia 4072, Australia.
¹¹ The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Victoria, Australia.
¹² Monash Biomedical Imaging, Monash University, Victoria, Australia.
¹³ School of Psychology, University of Adelaide, Adelaide, 5000, Australia.
¹⁴ Human Health, Health & Biosecurity, CSIRO, Adelaide, 5000, Australia.
¹⁵ Wellcome Centre for Human Neuroimaging, University College London, London, UK.
¹⁶ The University of Queensland, School of Psychology, St Lucia 4072, Australia.
¹⁷ Melbourne School of Psychological Sciences, The University of Melbourne.
¹⁸ Graeme Clark Institute for Biomedical Engineering, The University of Melbourne.
¹⁹ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
²⁰ Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA.
²¹ GIGA CRC In-Vivo Imaging, University of Liege, Liege, Belgium.
²² Functional Magnetic Resonance Imaging Core Facility (FMRIF), National Institute of Mental Health (NIMH), USA.
²³ Medical Scientist Training Program, Stony Brook University, Stony Brook, NY, United States of America.
²⁴ Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America.
²⁵ Techna Institute, University Health Network, Toronto, Canada.
²⁶ Department of Data Science and AI, Faculty of Information Technology, Monash University, Clayton VIC 3800, Australia.
²⁷ Grupo Neuropsicología y Conducta (GRUNECO), Facultad de Medicina, Universidad de Antioquia, Colombia.
²⁸ The University of Auckland, Auckland, 1010, New Zealand.
²⁹ Department of Psychology, Center for Perceptual Systems, Center for Theoretical and Computational Neuroscience, Center on Aging and Population Sciences, Center for Learning and Memory, The University of Texas at Austin, 108 E Dean Keeton St, Austin, TX 78712, USA.
³⁰ Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA.
³¹ Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Australia.
³² Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.
³³ McCausland Center for Brain Imaging, Department of Psychology, University of South Carolina, Columbia SC, 29208, USA.
³⁴ School of Psychology, University of Wollongong, Wollongong, 2522, Australia.
³⁵ The University of Queensland, Centre for Advanced Imaging, St Lucia 4072, Australia.
³⁶ Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Australia.
³⁷ Macquarie University, School of Psychological Sciences, North Ryde 2112, Australia.
³⁸ Department of Neuroscience, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia.
³⁹ Monash-Epworth Rehabilitation Research Centre, Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, 3168, Australia.

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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Abstract

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