QuNex recipes: Executable, human-readable workflows for reproducible neuroimaging research

18/06/2026

AI Summary

QuNex recipes provide executable, human-readable workflow definitions covering onboarding, preprocessing, and analysis for complete neuroimaging pipelines.
Integrated into containerised QuNex, recipes capture every step and parameter, and combine QuNex commands with custom scripts and external tools.
Full reproducibility requires only the QuNex version, the recipe file, and the data enabling one-command replication and standardised workflow sharing.

TL;DR (AI Generated)

To address these challenges, we introduce QuNex recipes, a framework for defining and executing complete neuroimaging workflows-encompassing data onboarding, preprocessing, and analysis-in a transparent, machine- and human-readable format.

Recipes are implemented as an integrated feature of the Quantitative Neuroimaging Environment & Toolbox (QuNex), a containerized, open-source platform for end-to-end multimodal and multi-species neuroimaging processing.

By providing a standardized way to describe and share workflows, recipes facilitate open exchange of best practices and reproducible methods within the neuroimaging community.

Basic summary

Imaging Neurosci (Camb). 2026 Jun 15;4:IMAG.a.1274. doi: 10.1162/IMAG.a.1274. eCollection 2026.

ABSTRACT

Preprocessing and analysis of neuroimaging data are technically demanding, often requiring a combination of multiple software tools, modality-specific pipelines, and extensive parameter tuning to match dataset characteristics. These complexities make it difficult to document workflows in sufficient detail to ensure complete transparency and reproducibility. To address these challenges, we introduce QuNex recipes, a framework for defining and executing complete neuroimaging workflows-encompassing data onboarding, preprocessing, and analysis-in a transparent, machine- and human-readable format. Recipes are implemented as an integrated feature of the Quantitative Neuroimaging Environment & Toolbox (QuNex), a containerized, open-source platform for end-to-end multimodal and multi-species neuroimaging processing. The recipes framework enables seamless integration of QuNex commands with custom scripts and external tools, capturing every processing step and parameter setting. A fully reproducible study can thus be shared and replicated by providing only (a) the QuNex version used, (b) the recipe file, and (c) the data. This approach standardizes workflow specification, enhances transparency, and enables one-command replication of complex neuroimaging analyses. By providing a standardized way to describe and share workflows, recipes facilitate open exchange of best practices and reproducible methods within the neuroimaging community.

PMID:42312086 | PMC:PMC13271150 | DOI:10.1162/IMAG.a.1274

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