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 Flandin; Kelly 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

doi:10.1038/s41592-023-02145-x

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

Nat Methods. 2024 Jan 8. doi: 10.1038/s41592-023-02145-x. Online ahead of print.

Authors

Angela I Renton^#^{1

2}, Thuy T Dao^#³, Tom Johnstone⁴, Oren Civier⁴, Ryan P Sullivan⁵, David J White⁴, Paris Lyons⁴, Benjamin M Slade⁴, David F Abbott⁶, Toluwani J Amos⁷, Saskia Bollmann³, Andy Botting⁸, Megan E J Campbell^{9

10}, Jeryn Chang¹¹, Thomas G Close⁵, Monika Dörig¹², Korbinian Eckstein³, Gary F Egan^{13

14}, Stefanie Evas^{15

16}, Guillaume Flandin¹⁷, Kelly G Garner^{18

19}, Marta I Garrido^{20

21}, Satrajit S Ghosh^{22

23}, Martin Grignard²⁴, Yaroslav O Halchenko²⁵, Anthony J Hannan⁶, Anibal S Heinsfeld²⁶, Laurentius Huber²⁷, Matthew E Hughes⁴, Jakub R Kaczmarzyk^{28

29}, Lars Kasper^{30

31}, Levin Kuhlmann³², Kexin Lou^{3

33}, Yorguin-Jose Mantilla-Ramos³⁴, Jason B Mattingley^{35

19}, Michael L Meier¹², Jo Morris⁸, Akshaiy Narayanan³⁶, Franco Pestilli²⁶, Aina Puce³⁷, Fernanda L Ribeiro³, Nigel C Rogasch^{13

38

39}, Chris Rorden⁴⁰, Mark M Schira⁴¹, Thomas B Shaw^{3

42

43}, Paul F Sowman⁴⁴, Gershon Spitz^{45

46}, Ashley W Stewart^{3

47}, Xincheng Ye³, Judy D Zhu⁴⁴, Aswin Narayanan⁴², Steffen Bollmann^{48

49

50

51}

Affiliations

¹ The University of Queensland, Queensland Brain Institute, St Lucia, Brisbane, Queensland, Australia. angie.renton23@gmail.com.
² The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia. angie.renton23@gmail.com.
³ The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.
⁴ Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.
⁵ The University of Sydney, School of Biomedical Engineering, Sydney, New South Wales, Australia.
⁶ The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia.
⁷ School of Life Science and Technology, University of Electronic Science and Technology, Chengdu, China.
⁸ Australian Research Data Commons (ARDC), Sydney, New South Wales, Australia.
⁹ School of Psychological Sciences, University of Newcastle, Newcastle, New South Wales, Australia.
¹⁰ Hunter Medical Research Institute Imaging Centre, Newcastle, New South Wales, Australia.
¹¹ The University of Queensland, School of Biomedical Sciences, St Lucia, Brisbane, Queensland, Australia.
¹² Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, University of Zurich, Zurich, Switzerland.
¹³ The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia.
¹⁴ Monash Biomedical Imaging, Monash University, Melbourne, Victoria, Australia.
¹⁵ School of Psychology, University of Adelaide, Adelaide, South Australia, Australia.
¹⁶ Human Health, Health & Biosecurity, CSIRO, Adelaide, South Australia, Australia.
¹⁷ Wellcome Centre for Human Neuroimaging, University College London, London, UK.
¹⁸ School of Psychology, University of New South Wales, Sydney, New South Wales, Australia.
¹⁹ The University of Queensland, School of Psychology, St Lucia, Brisbane, Queensland, Australia.
²⁰ Melbourne School of Psychological Sciences, he University of Melbourne, Melbourne, Victoria, Australia.
²¹ Graeme Clark Institute for Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia.
²² McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
²³ Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA.
²⁴ GIGA CRC In-Vivo Imaging, University of Liège, Liège, Belgium.
²⁵ Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA.
²⁶ Department of Psychology, Center for Perceptual Systems, Institute for Neuroscience, Center For Learning and Memory, The University of Texas at Austin, Austin, TX, USA.
²⁷ National Institute of Mental Health (NIMH), National Institutes Health, Bethesda, MD, USA.
²⁸ Department of Biomedical Informatics, Stony Brook University, New York, NY, USA.
²⁹ Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, New York, NY, USA.
³⁰ BRAIN-TO Lab, Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada.
³¹ Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland.
³² Department of Data Science and AI, Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia.
³³ Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
³⁴ Grupo Neuropsicología y Conducta (GRUNECO), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
³⁵ The University of Queensland, Queensland Brain Institute, St Lucia, Brisbane, Queensland, Australia.
³⁶ School of Computer Science, The University of Auckland, Auckland, New Zealand.
³⁷ Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA.
³⁸ Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
³⁹ Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.
⁴⁰ McCausland Center for Brain Imaging, Department of Psychology, University of South Carolina, Columbia, SC, USA.
⁴¹ School of Psychology, University of Wollongong, Wollongong, New South Wales, Australia.
⁴² The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia.
⁴³ Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
⁴⁴ Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia.
⁴⁵ Department of Neuroscience, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia.
⁴⁶ Monash-Epworth Rehabilitation Research Centre, Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia.
⁴⁷ ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, Queensland, Australia.
⁴⁸ The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au.
⁴⁹ The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au.
⁵⁰ ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au.
⁵¹ Queensland Digital Health Centre, The University of Queensland, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au.

^# Contributed equally.

PMID: 38191935
DOI: 10.1038/s41592-023-02145-x

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.