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

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

Brain Stimulation, Imaging And Cognition

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

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 language	English
Journal	Nature Methods
DOIs	https://doi.org/10.1038/s41592-023-02145-x
Publication status	Published or Issued - 8 Jan 2024

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Renton, A. I., Dao, T. T., Johnstone, T., Civier, O., Sullivan, R. P., White, D. J., Lyons, P., Slade, B. M., Abbott, D. F., Amos, T. J., Bollmann, S., Botting, A., Campbell, M. E. J., Chang, J., Close, T. G., Dörig, M., Eckstein, K., Egan, G. F., Evas, S., ... Bollmann, S. (2024). Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods. https://doi.org/10.1038/s41592-023-02145-x

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

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.",

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

note = "Funding Information: The ARDC invested in Neurodesk{\textquoteright}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. {\textquoteleft}Sam{\textquoteright} Peng for contributions to the first NeuroDesk precursor {\textquoteleft}Dicom2Cloud{\textquoteright} 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. Publisher Copyright: {\textcopyright} 2024, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2024",

month = jan,

day = "8",

doi = "10.1038/s41592-023-02145-x",

language = "English",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

}

Renton, AI, Dao, TT, Johnstone, T, Civier, O, Sullivan, RP, White, DJ, Lyons, P, Slade, BM, Abbott, DF, Amos, TJ, Bollmann, S, Botting, A, Campbell, MEJ, Chang, J, Close, TG, Dörig, M, Eckstein, K, Egan, GF, Evas, S, Flandin, G, Garner, KG, Garrido, MI, Ghosh, SS, Grignard, M, Halchenko, YO, Hannan, AJ, Heinsfeld, AS, Huber, L, Hughes, ME, Kaczmarzyk, JR, Kasper, L, Kuhlmann, L, Lou, K, Mantilla-Ramos, YJ, Mattingley, JB, Meier, ML, Morris, J, Narayanan, A, Pestilli, F, Puce, A, Ribeiro, FL, Rogasch, NC, Rorden, C, Schira, MM, Shaw, TB, Sowman, PF, Spitz, G, Stewart, AW, Ye, X, Zhu, JD, Narayanan, A & Bollmann, S 2024, 'Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging', Nature Methods. https://doi.org/10.1038/s41592-023-02145-x

TY - JOUR

T1 - Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

AU - Renton, Angela I.

AU - Dao, Thuy T.

AU - Johnstone, Tom

AU - Civier, Oren

AU - Sullivan, Ryan P.

AU - White, David J.

AU - Lyons, Paris

AU - Slade, Benjamin M.

AU - Abbott, David F.

AU - Amos, Toluwani J.

AU - Bollmann, Saskia

AU - Botting, Andy

AU - Campbell, Megan E.J.

AU - Chang, Jeryn

AU - Close, Thomas G.

AU - Dörig, Monika

AU - Eckstein, Korbinian

AU - Egan, Gary F.

AU - Evas, Stefanie

AU - Flandin, Guillaume

AU - Garner, Kelly G.

AU - Garrido, Marta I.

AU - Ghosh, Satrajit S.

AU - Grignard, Martin

AU - Halchenko, Yaroslav O.

AU - Hannan, Anthony J.

AU - Heinsfeld, Anibal S.

AU - Huber, Laurentius

AU - Hughes, Matthew E.

AU - Kaczmarzyk, Jakub R.

AU - Kasper, Lars

AU - Kuhlmann, Levin

AU - Lou, Kexin

AU - Mantilla-Ramos, Yorguin Jose

AU - Mattingley, Jason B.

AU - Meier, Michael L.

AU - Morris, Jo

AU - Narayanan, Akshaiy

AU - Pestilli, Franco

AU - Puce, Aina

AU - Ribeiro, Fernanda L.

AU - Rogasch, Nigel C.

AU - Rorden, Chris

AU - Schira, Mark M.

AU - Shaw, Thomas B.

AU - Sowman, Paul F.

AU - Spitz, Gershon

AU - Stewart, Ashley W.

AU - Ye, Xincheng

AU - Zhu, Judy D.

AU - Narayanan, Aswin

AU - Bollmann, Steffen

N1 - Funding Information: 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. Publisher Copyright: © 2024, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2024/1/8

Y1 - 2024/1/8

N2 - 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.

AB - 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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U2 - 10.1038/s41592-023-02145-x

DO - 10.1038/s41592-023-02145-x

M3 - Article

AN - SCOPUS:85181700402

SN - 1548-7091

JO - Nature Methods

JF - Nature Methods

ER -

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

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