A very simple, re-executable neuroimaging publication

doi:10.12688/f1000research.10783.2

. 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 Poline³, David B Keator⁴, Yaroslav O Halchenko⁵, Adam G Thomas⁶, Daniel A Kessler⁷, David N Kennedy⁸

Affiliations

¹ McGovern Institute for Brain Research, Massachusetts Institute of Technology: MIT, Cambridge, MA, USA.
² Department of Otology and Laryngology, Harvard Medical School, Boston, MA, USA.
³ Henry Wheeler Jr. Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
⁴ Department of Psychiatry and Human Behavior, Department of Computer Science, Department of Neurology, University of California, Irvine, Irvine, CA, USA.
⁵ Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA.
⁶ Data Science and Sharing Team, National Institute of Mental Health, Intramural Research Programs, Bethesda, MD, USA.
⁷ Department of Psychiatry and Department of Radiology, University of Michigan, Ann Arbor, MI, USA.
⁸ Eunice K. Shriver Center and Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA.

PMID: 28781753
PMCID: PMC5516225
DOI: 10.12688/f1000research.10783.2

A very simple, re-executable neuroimaging publication

Satrajit S Ghosh et al. F1000Res. 2017.

. 2017 Feb 10:6:124.

doi: 10.12688/f1000research.10783.2. eCollection 2017.

Authors

Satrajit S Ghosh^{1

2}, Jean-Baptiste Poline³, David B Keator⁴, Yaroslav O Halchenko⁵, Adam G Thomas⁶, Daniel A Kessler⁷, David N Kennedy⁸

Affiliations

¹ McGovern Institute for Brain Research, Massachusetts Institute of Technology: MIT, Cambridge, MA, USA.
² Department of Otology and Laryngology, Harvard Medical School, Boston, MA, USA.
³ Henry Wheeler Jr. Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
⁴ Department of Psychiatry and Human Behavior, Department of Computer Science, Department of Neurology, University of California, Irvine, Irvine, CA, USA.
⁵ Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA.
⁶ Data Science and Sharing Team, National Institute of Mental Health, Intramural Research Programs, Bethesda, MD, USA.
⁷ Department of Psychiatry and Department of Radiology, University of Michigan, Ann Arbor, MI, USA.
⁸ Eunice K. Shriver Center and Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA.

PMID: 28781753
PMCID: PMC5516225
DOI: 10.12688/f1000research.10783.2

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.

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Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

**Figure 1.. Example images from a subset of three of the subject image datasets used.**

**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

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References

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[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

[2] 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

[3] 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

[4] 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

[5] Ghosh SS, Halchenko Y, Poline JB, et al. : ReproNim - Simple Paper v1.0.0 [Data set]. Zenodo. 2017. Data Source - DOI

[6] Ghosh SS, Halchenko Y, Poline JB, et al. : ReproNim - Simple Paper v1.0.0 [Data set]. Zenodo. 2017. Data Source - DOI

[7] 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

[8] 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

[9] 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

[10] 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

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A very simple, re-executable neuroimaging publication

Affiliations

A very simple, re-executable neuroimaging publication

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

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References

Grants and funding

LinkOut - more resources

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