Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Feb 10:6:124.
doi: 10.12688/f1000research.10783.2. eCollection 2017.

A very simple, re-executable neuroimaging publication

Satrajit S Ghosh  1   2 , Jean-Baptiste Poline  3 , David B Keator  4 , Yaroslav O Halchenko  5 , Adam G Thomas  6 , Daniel A Kessler  7 , David N Kennedy  8
Affiliations

A very simple, re-executable neuroimaging publication

Satrajit S Ghosh et al. F1000Res. .

Abstract

Reproducible research is a key element of the scientific process. Re-executability of neuroimaging workflows that lead to the conclusions arrived at in the literature has not yet been sufficiently addressed and adopted by the neuroimaging community. In this paper, we document a set of procedures, which include supplemental additions to a manuscript, that unambiguously define the data, workflow, execution environment and results of a neuroimaging analysis, in order to generate a verifiable re-executable publication. Re-executability provides a starting point for examination of the generalizability and reproducibility of a given finding.

Keywords: Neuroimaging analysis; re-executable publication; reproducibility.

PubMed Disclaimer

Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Example images from a subset of three of the subject image datasets used.
Figure 2.
Figure 2.. Workflow diagram.
The sequence and dependence of processing events used in this example re-executable publication.
See this image and copyright information in PMC

References

    1. Biswal BB, Mennes M, Zuo XN, et al. : Toward discovery science of human brain function. Proc Natl Acad Sci U S A. 2010;107(10):4734–4739. 10.1073/pnas.0911855107 - DOI - PMC - PubMed
    1. Button KS, Ioannidis JP, Mokrysz C, et al. : Power failure: why small sample size undermines the reliability of neuroscience. Nat Rev Neurosci. 2013;14(5):365–376. 10.1038/nrn3475 - DOI - PubMed
    1. Ghosh SS, Halchenko Y, Poline JB, et al. : ReproNim - Simple Paper v1.0.0 [Data set]. Zenodo. 2017. Data Source - DOI
    1. Glatard T, Lewis LB, Ferreira da Silva R, et al. : Reproducibility of neuroimaging analyses across operating systems. Front Neuroinform. 2015;9:12. 10.3389/fninf.2015.00012 - DOI - PMC - PubMed
    1. Gorgolewski K, Burns CD, Madison C, et al. : Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python. Front Neuroinform. 2011;5:13. 10.3389/fninf.2011.00013 - DOI - PMC - PubMed