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

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

28 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	5
Journal	NATURE METHODS
Volume	21
Issue number	5
DOIs	https://doi.org/10.1038/s41592-023-02145-x
Publication status	Published - 1 May 2024
Externally published	Yes

Keywords

Neuroimaging
Neurodesk
neuroimaging software

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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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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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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.

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AU - Close, Thomas G.

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AU - Eckstein, Korbinian

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

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Keywords

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