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

Renton, A. I.; Dao, T. T.; Abbott, D. F.; Bollmann, S.; Campbell, M. E. J.; Chang, J.; Close, T. G.; Eckstein, K.; Egan, G. F.; Evas, S.; Garner, K. G.; Garrido, M. I.; Hannan, A. J.; Huber, R.; Johnstone, T.; Kaczmarzyk, J. R.; Kasper, L.; Kuhlmann, L.; Lou, K.; Lyons, P.; Mattingley, J. B.; Narayanan, A.; Pestilli, F.; Puce, A.; Ribeiro, F. L.; Rogasch, N. C.; Shaw, T. B.; Sowman, P. F.; Spitz, G.; Stewart, A.; Sullivan, R. P.; White, D. J.; Ye, X.; Zhu, J. D.

doi:10.1101/2022.12.23.521691

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bioRxiv · 10.1101/2022.12.23.521691

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

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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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Renton, A. I., Dao, T. T., Abbott, D. F., Bollmann, S., Campbell, M. E. J., Chang, J., Close, T. G., Eckstein, K., Egan, G. F., Evas, S., Garner, K. G., Garrido, M. I., Hannan, A. J., Huber, R., Johnstone, T., Kaczmarzyk, J. R., Kasper, L., Kuhlmann, L., Lou, K., Lyons, P., Mattingley, J. B., Narayanan, A., Pestilli, F., Puce, A., Ribeiro, F. L., Rogasch, N. C., Shaw, T. B., Sowman, P. F., Spitz, G., Stewart, A., Sullivan, R. P., White, D. J., Ye, X., Zhu, J. D.. 2022-12-23. Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging. https://doi.org/10.1101/2022.12.23.521691

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