A comprehensive framework to capture the arcana of neuroimaging analysis

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

Research output: Contribution to journalArticleResearchpeer-review

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.

Original languageEnglish
Pages (from-to)109-129
Number of pages21
JournalNeuroInformatics
Volume18
DOIs
Publication statusPublished - 2020

Keywords

  • Large-scale
  • Neuroimaging
  • Python
  • Repository
  • Reproducibility
  • Reusability
  • Workflows

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