Best practices in data analysis and sharing in neuroimaging using MRI

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Abstract

Given concerns about the reproducibility of scientific findings, neuroimaging must define best practices for data analysis, results reporting, and algorithm and data sharing to promote transparency, reliability and collaboration. We describe insights from developing a set of recommendations on behalf of the Organization for Human Brain Mapping and identify barriers that impede these practices, including how the discipline must change to fully exploit the potential of the world’s neuroimaging data.

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Most cited references 15

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Reproducible research in computational science.

Roger Peng (2011)

Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.

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Deriving reproducible biomarkers from multi-site resting-state data: An Autism-based example

Alexandre Abraham, Michael P Milham, Adriana Di Martino … (2017)

Resting-state functional Magnetic Resonance Imaging (R-fMRI) holds the promise to reveal functional biomarkers of neuropsychiatric disorders. However, extracting such biomarkers is challenging for complex multi-faceted neuropathologies, such as autism spectrum disorders. Large multi-site datasets increase sample sizes to compensate for this complexity, at the cost of uncontrolled heterogeneity. This heterogeneity raises new challenges, akin to those face in realistic diagnostic applications. Here, we demonstrate the feasibility of inter-site classification of neuropsychiatric status, with an application to the Autism Brain Imaging Data Exchange (ABIDE) database, a large (N=871) multi-site autism dataset. For this purpose, we investigate pipelines that extract the most predictive biomarkers from the data. These R-fMRI pipelines build participant-specific connectomes from functionally-defined brain areas. Connectomes are then compared across participants to learn patterns of connectivity that differentiate typical controls from individuals with autism. We predict this neuropsychiatric status for participants from the same acquisition sites or different, unseen, ones. Good choices of methods for the various steps of the pipeline lead to 67% prediction accuracy on the full ABIDE data, which is significantly better than previously reported results. We perform extensive validation on multiple subsets of the data defined by different inclusion criteria. These enables detailed analysis of the factors contributing to successful connectome-based prediction. First, prediction accuracy improves as we include more subjects, up to the maximum amount of subjects available. Second, the definition of functional brain areas is of paramount importance for biomarker discovery: brain areas extracted from large R-fMRI datasets outperform reference atlases in the classification tasks.

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Meta-analysis of neuroimaging data: a comparison of image-based and coordinate-based pooling of studies.

Gholamreza Salimi-Khorshidi, Stephen Smith, John R Keltner … (2009)

With the rapid growth of neuroimaging research and accumulation of neuroinformatic databases the synthesis of consensus findings using meta-analysis is becoming increasingly important. Meta-analyses pool data across many studies to identify reliable experimental effects and characterize the degree of agreement across studies. Coordinate-based meta-analysis (CBMA) methods are the standard approach, where each study entered into the meta-analysis has been summarized using only the (x, y, z) locations of peak activations (with or without activation magnitude) reported in published reports. Image-based meta-analysis (IBMA) methods use the full statistic images, and allow the use of hierarchical mixed effects models that account for differing intra-study variance and modeling of random inter-study variation. The purpose of this work is to compare image-based and coordinate-based meta-analysis methods applied to the same dataset, a group of 15 fMRI studies of pain, and to quantify the information lost by working only with the coordinates of peak activations instead of the full statistic images. We apply a 3-level IBMA mixed model for a "mega-analysis", and highlight important considerations in the specification of each model and contrast. We compare the IBMA result to three CBMA methods: ALE (activation likelihood estimation), KDA (kernel density analysis) and MKDA (multi-level kernel density analysis), for various CBMA smoothing parameters. For the datasets considered, we find that ALE at sigma=15 mm, KDA at rho=25-30 mm and MKDA at rho=15 mm give the greatest similarity to the IBMA result, and that ALE was the most similar for this particular dataset, though only with a Dice similarity coefficient of 0.45 (Dice measure ranges from 0 to 1). Based on this poor similarity, and the greater modeling flexibility afforded by hierarchical mixed models, we suggest that IBMA is preferred over CBMA. To make IBMA analyses practical, however, the neuroimaging field needs to develop an effective mechanism for sharing image data, including whole-brain images of both effect estimates and their standard errors.

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Author and article information

Journal

Journal ID (nlm-journal-id): 9809671

Journal ID (pubmed-jr-id): 21092

Journal ID (nlm-ta): Nat Neurosci

Journal ID (iso-abbrev): Nat. Neurosci.

Title: Nature neuroscience

ISSN (Print): 1097-6256

ISSN (Electronic): 1546-1726

Publication date Nihms-submitted: 20 May 2017

Publication date (Print): 23 February 2017

Publication date PMC-release: 23 February 2018

Volume: 20

Issue: 3

Pages: 299-303

Affiliations

[1 ]University of Warwick, Coventry, UK

[2 ]McGill University, Montreal, Canada

[3 ]Montreal Neurological Institute, Montreal, Canada

[4 ]Institute of Neuroscience and Medicine (INM-1), Jülich Research Center, Jülich, Germany

[5 ]Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany

[6 ]Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada

[7 ]Otto-von-Guericke-University, Magdeburg, Germany

[8 ]Center for Behavioral Brain Sciences, Magdeburg, Germany

[9 ]MRC Cognition and Brain Sciences Unit, Cambridge, UK

[10 ]Child Mind Institute, New York, New York, USA

[11 ]Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York, USA

[12 ]Stanford University, Stanford, California, USA

[13 ]University of California, Berkeley, California, USA

[14 ]NEUROingenia Clinical and Research Center, Mexico City, Mexico

[15 ]Inria, Paris-Saclay University, Paris, France

[16 ]Washington University in St. Louis, St. Louis, Missouri, USA

[17 ]Erasmus University Medical Center, Rotterdam, The Netherlands

[18 ]National University of Singapore, Singapore

Author notes

Correspondence should be addressed to ( t.e.nichols@ 123456warwick.ac.uk )

Article

Accession ID: PMC5685169 Pmcid ID: PMC5685169 Pmc-uid ID: 5685169 Manuscript ID: nihpa876813

DOI: 10.1038/nn.4500

PMC ID: 5685169

PubMed ID: 28230846

SO-VID: cdd3171a-9b25-4eef-b54b-cfd8e3ab8e48

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Reprints and permissions information is available online at http://www.nature.com/reprints/index.html.

Best practices in data analysis and sharing in neuroimaging using MRI

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Good practices in (cog-neuro) science and science communication

Most cited references 15

Reproducible research in computational science.

Deriving reproducible biomarkers from multi-site resting-state data: An Autism-based example

Meta-analysis of neuroimaging data: a comparison of image-based and coordinate-based pooling of studies.

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