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QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research.

Jure Demšar1,2, Aleksij Kraljič2, Andraž Matkovič2,3,4

  • 1Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.

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Summary

QuNex recipes simplify complex neuroimaging data analysis by providing a transparent framework for reproducible workflows. This ensures detailed documentation and easy replication of neuroimaging studies.

Keywords:
data analysisdata processingneuroimagingreproducibility

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Area of Science:

  • Neuroimaging
  • Computational Neuroscience
  • Data Science

Background:

  • Neuroimaging data preprocessing and analysis are complex, requiring multiple tools and parameter tuning.
  • Current methods often lack sufficient detail for complete transparency and reproducibility.
  • This complexity hinders the sharing and replication of neuroimaging workflows.

Purpose of the Study:

  • To introduce QuNex recipes, a framework for defining and executing complete neuroimaging workflows.
  • To enhance transparency, reproducibility, and standardization in neuroimaging data processing.
  • To facilitate the seamless integration of various tools and custom scripts within a unified platform.

Main Methods:

  • Developed QuNex recipes as an integrated feature of the Quantitative Neuroimaging Environment & Toolbox (QuNex).
  • Recipes define and execute end-to-end neuroimaging workflows in a machine- and human-readable format.
  • The framework captures all processing steps and parameter settings for complete documentation.

Main Results:

  • QuNex recipes enable transparent, machine- and human-readable definition of neuroimaging workflows.
  • The framework allows seamless integration of QuNex commands, custom scripts, and external tools.
  • Sharing the QuNex version, recipe file, and data allows for one-command replication of studies.

Conclusions:

  • QuNex recipes standardize workflow specification and enhance transparency in neuroimaging research.
  • This framework facilitates the reproducible sharing of complex neuroimaging analyses.
  • Recipes promote the open exchange of best practices and reproducible methods within the neuroimaging community.