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^*

^*Corresponding author for this work

School of Psychological Sciences

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

29 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
Pages (from-to)	804-808
Number of pages	13
Journal	Nature Methods
Volume	21
Issue number	5
Early online date	8 Jan 2024
DOIs	https://doi.org/10.1038/s41592-023-02145-x
Publication status	Published - May 2024

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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, 21(5), 804-808. 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",

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

language = "English",

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pages = "804--808",

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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, vol. 21, no. 5, pp. 804-808. https://doi.org/10.1038/s41592-023-02145-x

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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

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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

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VL - 21

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JO - Nature Methods

JF - Nature Methods

IS - 5

ER -

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

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