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Towards structured sharing of raw and derived neuroimaging data across existing resources [article]

D. B. Keator, K. Helmer, J. Steffener, J. A. Turner, T. G. M. Van Erp, S. Gadde, N. Ashish, G. A. Burns, B. N. Nichols, S. S. Ghosh
2013 arXiv   pre-print
We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources.  ...  We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging  ...  The International Neuroinformatics Coordinating Facility provided financial support for some of the work reported in this article (to Satrajit Ghosh).  ... 
arXiv:1209.5922v3 fatcat:pcebf7inybfstkgkf6pfwrny7y

Towards structured sharing of raw and derived neuroimaging data across existing resources

D.B. Keator, K. Helmer, J. Steffener, J.A. Turner, T.G.M. Van Erp, S. Gadde, N. Ashish, G.A. Burns, B.N. Nichols
2013 NeuroImage  
We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources.  ...  We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging  ...  The International Neuroinformatics Coordinating Facility provided financial support for some of the work reported in this article (to Satrajit Ghosh).  ... 
doi:10.1016/j.neuroimage.2013.05.094 pmid:23727024 pmcid:PMC4028152 fatcat:enap2ihyhzfdfpz3gmtzqlqgna

Is it time to re-prioritize neuroimaging databases and digital repositories?

John Darrell Van Horn, Arthur W. Toga
2009 NeuroImage  
In this article, we review the progress made in neuroimaging databases, their role in data sharing, data management, potential for the construction of brain atlases, recording data provenance, and value  ...  In any individual research article, several tens of gigabytes-worth of data may be represented -collected across normal and patient samples.  ...  resources.  ... 
doi:10.1016/j.neuroimage.2009.03.086 pmid:19371790 pmcid:PMC2754579 fatcat:qxjviytffrexbf7wrn2xfkrns4

Human neuroimaging as a "Big Data" science

John Darrell Van Horn, Arthur W. Toga
2013 Brain Imaging and Behavior  
Yet few, if any, common solutions exist to support the science of neuroimaging.  ...  sharing issues; infrastructural challenges for multi-site, multi-datatype archiving; and the means by which to explore and mine these data.  ...  We express our gratitude the faculty and staff of the Laboratory of Neuro Imaging (LONI) at the University of California Los Angeles.  ... 
doi:10.1007/s11682-013-9255-y pmid:24113873 pmcid:PMC3983169 fatcat:vrbn7rrx2zbsvah6c5hssu5upa

Offering to Share: How to Put Heads Together in Autism Neuroimaging

Matthew K. Belmonte, John C. Mazziotta, Nancy J. Minshew, Alan C. Evans, Eric Courchesne, Stephen R. Dager, Susan Y. Bookheimer, Elizabeth H. Aylward, David G. Amaral, Rita M. Cantor, Diane C. Chugani, Anders M. Dale (+12 others)
2007 Journal of Autism and Developmental Disorders  
We outline the desiderata for a data-sharing scheme that combines imaging with other measures of phenotype and with genetics, defines requirements for comparability of derived data and recommendations  ...  Data sharing in autism neuroimaging presents scientific, technical, and social obstacles.  ...  Acknowledgements This statement is the product of the Neuroimaging Summit convened at the University of California Los Angeles, 23-24 January 2006, by Cure Autism Now.  ... 
doi:10.1007/s10803-006-0352-2 pmid:17347882 pmcid:PMC3076291 fatcat:4rhdtfb3fnegnfmb5xvzith4ve

Cognitive neuroscience 2.0: building a cumulative science of human brain function

Tal Yarkoni, Russell A. Poldrack, David C. Van Essen, Tor D. Wager
2010 Trends in Cognitive Sciences  
., NIH awards NIMH R01MH076136 and NIDA R01DA027794 to T.D.W., NIH award R01MH082795 to R.A.P., and NIH award R01MH60974 to D.V.E.  ...  Using these systems, data and code could be shared for each step of an analysis, along with raw data. Integration of ontologies and data sharing methods with fMRI analysis software.  ...  Deployment of massive data repositories capable of storing and serving raw data from 10 s of 1000 s of neuroimaging studies.  ... 
doi:10.1016/j.tics.2010.08.004 pmid:20884276 pmcid:PMC2963679 fatcat:bumvfpn56nfpbpxpbq4pjby2vu

Next Steps in Data Publishing

David N. Kennedy, Giorgio A. Ascoli, Erik De Schutter
2011 Neuroinformatics  
-How were the 'raw' data collected? In principle, a data release may contain both 'raw' and 'derived' sets of measures.  ...  Advancing the publication value of data collection itself, and promoting data sharing through data publication, we can exert a 'positive pressure' towards even more active data sharing and dissemination  ... 
doi:10.1007/s12021-011-9131-0 fatcat:u3hwyu6wljbbvkbos4v7unzd4q

Improving functional magnetic resonance imaging reproducibility

Cyril Pernet, Jean-Baptiste Poline
2015 GigaScience  
Conclusion: Only by sharing experiments, data, metadata, derived data and analysis workflows will neuroimaging establish itself as a true data science.  ...  All of these steps require researchers to move towards a more open science, in which all aspects of the experimental method are documented and shared.  ...  NeuroImaging Tool and Resources Clearinghouse (http://www.nitrc.org/), is a web resource that "facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses  ... 
doi:10.1186/s13742-015-0055-8 pmid:25830019 pmcid:PMC4379514 fatcat:3zjrgkuicrcyhib6yo4zfh2rdm

The informatics core of the Alzheimer's Disease Neuroimaging Initiative

Arthur W. Toga, Karen L. Crawford
2010 Alzheimer's & Dementia  
, and disseminate data and results.  ...  The Alzheimer's Diseases Neuroimaging Initiative project has brought together geographically distributed investigators, each collecting data on the progression of Alzheimer's disease.  ...  Acknowledgments Data used in preparing this article were obtained from the Alzheimer's Disease Neuroimaging Initiative database (www.loni.ucla.edu/ADNI).  ... 
doi:10.1016/j.jalz.2010.03.001 pmid:20451873 pmcid:PMC2927123 fatcat:ox4ibuy5zfb3bpay7f3nkpaapy

MEG-BIDS: an extension to the Brain Imaging Data Structure for magnetoencephalography [article]

Julia Guiomar Niso Galan, Krzysztof Jacek Gorgolewski, Elizabeth Bock, Teon L. Brooks, Guillaume Flandin, Alexandre Gramfort, Richard N. Henson, Mainak Jas, Vladimir Litvak, Jeremy Moreau, Robert Oostenveld, Jan-Mathijs Schoffelen (+3 others)
2017 bioRxiv   pre-print
With MEG-BIDS and a growing range of software adopting the standard, the MEG community has a solution to minimize curation overheads, reduce data handling errors and optimize usage of computational resources  ...  Despite the lack of standard data format for MEG, MEG-BIDS is a principled solution to store, organize and share the typically-large data volumes produced.  ...  by a Discovery Grant from the National Science and Engineering Research Council of Canada, the NIH (2R01EB009048-05) and a Platform Support Grant from the Brain Canada Foundation to Sylvain Baillet.  ... 
doi:10.1101/172684 fatcat:edwjx7fhazeztpu54gqmjvedn4

Connectomics and new approaches for analyzing human brain functional connectivity

R Cameron Craddock, Rosalia L Tungaraza, Michael P Milham
2015 GigaScience  
Additionally it provides information about open science resources consisting of raw and preprocessed data to help interested researchers get started.  ...  The number and complexity of functional interactions within the connectome and the large amounts of data required to study them position functional connectivity research as a "big data" problem.  ...  Anders Eklund and Dr. Xin Di for their useful comments, which improved the manuscript.  ... 
doi:10.1186/s13742-015-0045-x pmid:25810900 pmcid:PMC4373299 fatcat:5rmlp74mbffudp7ipo4sgobxea

Data sharing in neuroimaging research

Jean-Baptiste Poline, Janis L. Breeze, Satrajit Ghosh, Krzysztof Gorgolewski, Yaroslav O. Halchenko, Michael Hanke, Christian Haselgrove, Karl G. Helmer, David B. Keator, Daniel S. Marcus, Russell A. Poldrack, Yannick Schwartz (+2 others)
2012 Frontiers in Neuroinformatics  
It is hoped that such tools will allow researchers to easily share raw, processed, and derived neuroimaging data, with appropriate metadata and provenance records, and will improve the reproducibility  ...  A trend toward increased sharing of neuroimaging data has emerged in recent years. Nevertheless, a number of barriers continue to impede momentum.  ...  Although some resources have emerged to help find shared neuroimaging data through federation or mediation (e.g., NIF, NITRC), most cognitive researchers cannot rely on existing shared data to pursue their  ... 
doi:10.3389/fninf.2012.00009 pmid:22493576 pmcid:PMC3319918 fatcat:f4cgaldeuraavmcnxqrsisdebe

Brain Predictability toolbox: a Python library for neuroimaging based machine learning [article]

Sage Hahn, Dekang Yuan, Wesley Thompson, Max M Owens, Nicholas Allgaier, Hugh Garavan
2020 arXiv   pre-print
variables) and neuroimaging specific derived data (e.g., brain volumes and surfaces).  ...  Brain Predictability toolbox (BPt) represents a unified framework of machine learning (ML) tools designed to work with both tabulated data (in particular brain, psychiatric, behavioral, and physiological  ...  We would further like to thank the Data Analysis and Informatic Core of the ABCD Study who provided the structure of the code in which the web interface application was developed from.  ... 
arXiv:2011.01715v1 fatcat:uqrn7pelrfcadh5mlokm3wbugi

BIOMIST: A Platform for Biomedical Data Lifecycle Management of Neuroimaging Cohorts

Marianne Allanic, Pierre-Yves Hervé, Cong-Cuong Pham, Myriam Lekkal, Alexandre Durupt, Thierry Brial, Arthur Grioche, Nada Matta, Philippe Boutinaud, Benoit Eynard, Marc Joliot
2017 Frontiers in ICT  
and access policies, ensuring traceability and sharing data across different labs-are actually strikingly similar to those already expressed by the manufacturing industry.  ...  imaging-Share cohort acquisition of 2,000 participants.  ...  "Mapping Strategy for Data Import, " "The DIMP Method for Integration of Processing Pipelines, " "Implementation, " and "Application"; C-CP worked on Sections "Querying Strategies" and "Implementation"  ... 
doi:10.3389/fict.2016.00035 fatcat:7riec4yeorbyjlcemjab5idwkq

Toward open sharing of task-based fMRI data: the OpenfMRI project

Russell A. Poldrack, Deanna M. Barch, Jason P. Mitchell, Tor D. Wager, Anthony D. Wagner, Joseph T. Devlin, Chad Cumba, Oluwasanmi Koyejo, Michael P. Milham
2013 Frontiers in Neuroinformatics  
behind other areas of bioscience in the development of data sharing resources.  ...  The large-scale sharing of task-based functional neuroimaging data has the potential to allow novel insights into the organization of mental function in the brain, but the field of neuroimaging has lagged  ...  Thanks to Tom Schonberg, Chris Gorgolewski, and Jean-Baptise Poline, Laurens van der Maaten, and Jack Van Horn for helpful comments and Natalie Picchetti for assistance with data analysis.  ... 
doi:10.3389/fninf.2013.00012 pmid:23847528 pmcid:PMC3703526 fatcat:iydcpisyebdmjkvbd2dyqbefkm
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