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A Comprehensive Framework to Capture the Arcana of Neuroimaging Analysis

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Abstract

Mastering the “arcana of neuroimaging analysis”, the obscure knowledge required to apply an appropriate combination of software tools and parameters to analyse a given neuroimaging dataset, is a time consuming process. Therefore, it is not typically feasible to invest the additional effort required generalise workflow implementations to accommodate for the various acquisition parameters, data storage conventions and computing environments in use at different research sites, limiting the reusability of published workflows. We present a novel software framework, Abstraction of Repository-Centric ANAlysis (Arcana), which enables the development of complex, “end-to-end” workflows that are adaptable to new analyses and portable to a wide range of computing infrastructures. Analysis templates for specific image types (e.g. MRI contrast) are implemented as Python classes, which define a range of potential derivatives and analysis methods. Arcana retrieves data from imaging repositories, which can be BIDS datasets, XNAT instances or plain directories, and stores selected derivatives and associated provenance back into a repository for reuse by subsequent analyses. Workflows are constructed using Nipype and can be executed on local workstations or in high performance computing environments. Generic analysis methods can be consolidated within common base classes to facilitate code-reuse and collaborative development, which can be specialised for study-specific requirements via class inheritance. Arcana provides a framework in which to develop unified neuroimaging workflows that can be reused across a wide range of research studies and sites.

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Acknowledgements

The authors acknowledge the facilities and scientific and technical assistance of the National Imaging Facility, a National Collaborative Research Infrastructure Strategy (NCRIS) capability, at Monash Biomedical Imaging, Monash University. The “transparent repository” feature of Arcana was inspired by in-house software written by Parnesh Raniga while he was employed at Monash University prior to 2016.

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Authors and Affiliations

  1. Monash Biomedical Imaging, Monash University, Melbourne, Australia

    Thomas G. Close, Phillip G. D. Ward, Francesco Sforazzini, Zhaolin Chen & Gary F. Egan

  2. Australian National Imaging Facility, Brisbane, Australia

    Thomas G. Close

  3. Australian Research Council Centre of Excellence for integrative Brain Function, Melbourne, Australia

    Phillip G. D. Ward & Gary F. Egan

  4. Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Melbourne, Australia

    Phillip G. D. Ward & Gary F. Egan

  5. Department of Electrical and Computer Systems Engineering, Monash University, Melbourne, Australia

    Zhaolin Chen

  6. Monash eResearch Centre, Monash University, Melbourne, Australia

    Wojtek Goscinski

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  1. Thomas G. Close
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Correspondence to Thomas G. Close.

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Close, T.G., Ward, P.G.D., Sforazzini, F. et al. A Comprehensive Framework to Capture the Arcana of Neuroimaging Analysis. Neuroinform 18, 109–129 (2020). https://doi.org/10.1007/s12021-019-09430-1

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