# Neuroimaging article reexecution and reproduction assessment system

## TL;DR

This paper introduces a system for making neuroimaging research articles fully reexecutable and reproducible, enhancing transparency and trust in scientific results.

## Contribution

The paper presents a robust and modular system for reexecuting neuroimaging articles and outlines best practices for achieving reproducibility.

## Key findings

- A modular reexecution system was developed to enable end-to-end article regeneration from original data.
- The system supports reproducibility assessments through statistical metrics and visual divergence highlighting.
- Best practices for reexecution were identified and applied to mitigate common challenges.

## Abstract

The value of research articles is increasingly contingent on complex data analysis results which substantiate their claims. Compared to data production, data analysis more readily lends itself to a higher standard of transparency and repeated operator-independent execution. This higher standard can be approached via fully reexecutable research outputs, which contain the entire instruction set for automatic end-to-end generation of an entire article from the earliest feasible provenance point. In this study, we make use of a peer-reviewed neuroimaging article which provides complete but fragile reexecution instructions, as a starting point to draft a new reexecution system which is both robust and portable. We render this system modular as a core design aspect, so that reexecutable article code, data, and environment specifications could potentially be substituted or adapted. In conjunction with this system, which forms the demonstrative product of this study, we detail the core challenges with full article reexecution and specify a number of best practices which permitted us to mitigate them. We further show how the capabilities of our system can subsequently be used to provide reproducibility assessments, both via simple statistical metrics and by visually highlighting divergent elements for human inspection. We argue that fully reexecutable articles are thus a feasible best practice, which can greatly enhance the understanding of data analysis variability and the trust in results. Lastly, we comment at length on the outlook for reexecutable research outputs and encourage re-use and derivation of the system produced herein.