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An open resource for nonhuman primate imaging

Michael P. Milham, Lei Ai, Bonhwang Koo, Ting Xu, Fabien Balezeau, Mark G. Baxter, Paula L. Croxson, Christienne G. Damatac, Noam Harel, Winrich Freiwald, Timothy D. Griffiths, Stefan Everling, Benjamin Jung, Sabine Kastner, David A. Leopold, Rogier B. Mars, Ravi S. Menon, Adam Messinger, John H. Morrison, Jennifer Nacef, Jamie Nagy, Michael Ortiz Rios, Christopher I. Petkov, Mark Pinsk, Colline Poirier, Reza Rajimehr, Matthew F.S Rushworth, Brian E. Russ, Michael Schmid, Caspar M. Schwiedrzik, Jerome Sallet, Jakob Seidlitz, Leslie Ungerleider, Alexander Thiele, Doris Tsao, Essa Yacoub, Frank Ye, Wilbert Zarco, Daniel S. Margulies, Charles Schroeder
doi: https://doi.org/10.1101/227462
Michael P. Milham
1Center for the Developing Brain, Child Mind Institute, New York, NY, USA
2Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
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Lei Ai
1Center for the Developing Brain, Child Mind Institute, New York, NY, USA
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Bonhwang Koo
1Center for the Developing Brain, Child Mind Institute, New York, NY, USA
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Ting Xu
1Center for the Developing Brain, Child Mind Institute, New York, NY, USA
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Fabien Balezeau
1Center for the Developing Brain, Child Mind Institute, New York, NY, USA
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Mark G. Baxter
4Department of Neuroscience, Mount Sinai School of Medicine, New York, NY, USA
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Paula L. Croxson
4Department of Neuroscience, Mount Sinai School of Medicine, New York, NY, USA
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Christienne G. Damatac
5Donders Institute for Brain, Cognition and Behavior, Nijmegen, Netherlands
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Noam Harel
6Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA
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Winrich Freiwald
7Laboratory of Neural Systems, The Rockefeller University, New York, NY, USA
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Timothy D. Griffiths
3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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Stefan Everling
8Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, Ontario, Canada
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Benjamin Jung
9Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, MD, USA
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Sabine Kastner
10Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
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David A. Leopold
11Section on Cognitive Neurophysiology and Imaging, National Institute of Mental Health, Bethesda, MD, USA
12Neurophysiology Imaging Facility, National Institute of Mental Health, National Institute of Neurological Disorders and Stroke, National Eye Institute, Bethesda, MD, USA
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Rogier B. Mars
5Donders Institute for Brain, Cognition and Behavior, Nijmegen, Netherlands
13Wellcome Centre for Integrative Neuroimaging, Centre for Functional MRI of the Brain (FMRIB), Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
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Ravi S. Menon
8Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, Ontario, Canada
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Adam Messinger
9Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, MD, USA
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John H. Morrison
15California National Primate Research Center, Davis, CA, USA
16Department of Neurology, School of Medicine, University of California, Davis, CA, USA
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Jennifer Nacef
3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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Jamie Nagy
4Department of Neuroscience, Mount Sinai School of Medicine, New York, NY, USA
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Michael Ortiz Rios
3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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Christopher I. Petkov
3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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Mark Pinsk
10Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
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Colline Poirier
3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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Reza Rajimehr
17McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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Matthew F.S Rushworth
13Wellcome Centre for Integrative Neuroimaging, Centre for Functional MRI of the Brain (FMRIB), Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
14Wellcome Centre for Integrative Neuroimaging, Department of Experimental Psychology, University of Oxford, Oxford, UK
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Brian E. Russ
11Section on Cognitive Neurophysiology and Imaging, National Institute of Mental Health, Bethesda, MD, USA
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Michael Schmid
3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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Caspar M. Schwiedrzik
7Laboratory of Neural Systems, The Rockefeller University, New York, NY, USA
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Jerome Sallet
14Wellcome Centre for Integrative Neuroimaging, Department of Experimental Psychology, University of Oxford, Oxford, UK
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Jakob Seidlitz
9Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, MD, USA
18Developmental Neurogenomics Unit, National Institute of Mental Health, Bethesda, MD, USA
19Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK
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Leslie Ungerleider
9Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, MD, USA
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Alexander Thiele
3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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Doris Tsao
20Department of Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA
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Essa Yacoub
6Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA
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Frank Ye
11Section on Cognitive Neurophysiology and Imaging, National Institute of Mental Health, Bethesda, MD, USA
12Neurophysiology Imaging Facility, National Institute of Mental Health, National Institute of Neurological Disorders and Stroke, National Eye Institute, Bethesda, MD, USA
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Wilbert Zarco
7Laboratory of Neural Systems, The Rockefeller University, New York, NY, USA
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Daniel S. Margulies
21Max Planck Research Group for Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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Charles Schroeder
2Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
22Department of Neurological Surgery, Columbia University College of Physicians and Surgeons, New York, NY, USA
23Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
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ABSTRACT

Non-human primate neuroimaging is a rapidly growing area of research that promises to transform and scale translational and cross-species comparative neuroscience.

Unfortunately, the technological and methodological advances of the past two decades have outpaced the accrual of data, which is particularly challenging given the relatively few centers that have the necessary facilities and capabilities. The PRIMate Data Exchange (PRIME-DE) addresses this challenge by aggregating independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI). Here, we present the rationale, design and procedures for the PRIME-DE consortium, as well as the initial release, consisting of 13 independent data collections aggregated across 11 sites (total = 98 macaque monkeys). We also outline the unique pitfalls and challenges that should be considered in the analysis of the non-human primate MRI datasets, including providing automated quality assessment of the contributed datasets.

  • LIST OF ABBREVIATIONS

    dMRI
    : diffusion magnetic resonance imaging
    DUA
    : data usage agreement
    fMRI
    : functional magnetic resonance imaging
    INDI
    : International Neuroimaging Data-sharing Initiative
    MRI
    : magnetic resonance imaging
    NIMH
    : National Institute of Mental Health
    NIH
    : National Institutes of Health
    NMT
    : National Institute of Mental Health Macaque Template
    QA
    : quality assurance
    QAP
    : quality assurance protocol
    sMRI
    : structural magnetic resonance imaging
    FA
    : flip angle
    TE
    : echo time
    TR
    : repetition time
    BW
    : bandwidth per pixel
    ES
    : echo spacing
    PA
    : parallel acquisition
    PF
    : Partial Fourier (half scan)
    PE
    : Phase encoding
    FS
    : fat suppression
    SO
    : slice orientation
    SA
    : slice acquisition order
    Gap
    : gap between slices
    SO
    : Slice orientation
    PE
    : phase encoding
    RO
    : read out direction
    Nacq
    : number of volumes collected
    Ndisc
    : number of initial volumes discarded by the scanner
    TA
    : acquisition time
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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    Posted November 30, 2017.
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    An open resource for nonhuman primate imaging
    Michael P. Milham, Lei Ai, Bonhwang Koo, Ting Xu, Fabien Balezeau, Mark G. Baxter, Paula L. Croxson, Christienne G. Damatac, Noam Harel, Winrich Freiwald, Timothy D. Griffiths, Stefan Everling, Benjamin Jung, Sabine Kastner, David A. Leopold, Rogier B. Mars, Ravi S. Menon, Adam Messinger, John H. Morrison, Jennifer Nacef, Jamie Nagy, Michael Ortiz Rios, Christopher I. Petkov, Mark Pinsk, Colline Poirier, Reza Rajimehr, Matthew F.S Rushworth, Brian E. Russ, Michael Schmid, Caspar M. Schwiedrzik, Jerome Sallet, Jakob Seidlitz, Leslie Ungerleider, Alexander Thiele, Doris Tsao, Essa Yacoub, Frank Ye, Wilbert Zarco, Daniel S. Margulies, Charles Schroeder
    bioRxiv 227462; doi: https://doi.org/10.1101/227462
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    An open resource for nonhuman primate imaging
    Michael P. Milham, Lei Ai, Bonhwang Koo, Ting Xu, Fabien Balezeau, Mark G. Baxter, Paula L. Croxson, Christienne G. Damatac, Noam Harel, Winrich Freiwald, Timothy D. Griffiths, Stefan Everling, Benjamin Jung, Sabine Kastner, David A. Leopold, Rogier B. Mars, Ravi S. Menon, Adam Messinger, John H. Morrison, Jennifer Nacef, Jamie Nagy, Michael Ortiz Rios, Christopher I. Petkov, Mark Pinsk, Colline Poirier, Reza Rajimehr, Matthew F.S Rushworth, Brian E. Russ, Michael Schmid, Caspar M. Schwiedrzik, Jerome Sallet, Jakob Seidlitz, Leslie Ungerleider, Alexander Thiele, Doris Tsao, Essa Yacoub, Frank Ye, Wilbert Zarco, Daniel S. Margulies, Charles Schroeder
    bioRxiv 227462; doi: https://doi.org/10.1101/227462

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