Machine Learning for Large-Scale Quality Control of 3D Shape Models in Neuroimaging.

Journal: Machine learning in medical imaging. MLMI (Workshop)
Published Date: Sep 7, 2017

Abstract

As very large studies of complex neuroimaging phenotypes become more common, human quality assessment of MRI-derived data remains one of the last major bottlenecks. Few attempts have so far been made to address this issue with machine learning. In this work, we optimize predictive models of quality for meshes representing deep brain structure shapes. We use standard vertex-wise and global shape features computed homologously across 19 cohorts and over 7500 human-rated subjects, training kernelized Support Vector Machine and Gradient Boosted Decision Trees classifiers to detect meshes of failing quality. Our models generalize across datasets and diseases, reducing human workload by 30-70%, or equivalently hundreds of human rater hours for datasets of comparable size, with recall rates approaching inter-rater reliability.

Authors

  • Dmitry Petrov
    Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, University of Southern California, Marina Del Rey, CA, USA.
  • Boris A Gutman
    Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, University of Southern California, Marina Del Rey, CA, USA.
  • Shih-Hua Julie Yu
    Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, University of Southern California, Marina Del Rey, CA, USA.
  • Theo G M van Erp
    Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA.
  • Jessica A Turner
    Psychology Department & Neuroscience Institute, Georgia State University, Atlanta GA, USA.
  • Lianne Schmaal
    Orygen, The National Centre of Excellence in Youth Mental Health, Melbourne, Australia.
  • Dick Veltman
    Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands.
  • Lei Wang
    Department of Nursing, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
  • Kathryn Alpert
    Department of Psychiatry, Northwestern University, Chicago, IL, USA.
  • Dmitry Isaev
    Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, University of Southern California, Marina Del Rey, CA, USA.
  • Artemis Zavaliangos-Petropulu
    Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, University of Southern California, Marina Del Rey, CA, USA.
  • Christopher R K Ching
    Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, University of Southern California, Marina Del Rey, CA, USA.
  • Vince Calhoun
    The Mind Research Network, Albuquerque, NM, USA.
  • David Glahn
    Yale University School of Medicine, New Haven, CT, USA.
  • Theodore D Satterthwaite
    Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
  • Ole Andreas Andreasen
    CoE NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
  • Stefan Borgwardt
    Department of Psychiatry, University of Basel, Basel, Switzerland.
  • Fleur Howells
    MRC Unit on Risk & Resilience to Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
  • Nynke Groenewold
    MRC Unit on Risk & Resilience to Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
  • Aristotle Voineskos
    Centre for Addiction and Mental Health, Toronto, Canada.
  • Joaquim Radua
    FIDMAG Germanes Hospitalaries Research Foundation, Barcelona, Spain.
  • Steven G Potkin
    Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA.
  • Benedicto Crespo-Facorro
    Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain.
  • Diana Tordesillas-Gutiérrez
    University Hospital Marqués de Valdecilla, IDIVAL, Department of Psychiatry, School of Medicine, University of Cantabria, Santander, Spain.
  • Li Shen
    Department of Clinical Pharmacy, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
  • Irina Lebedeva
    Mental Health Research Center, Moscow, Russia.
  • Gianfranco Spalletta
    Laboratory of Neuropsychiatry, Santa Lucia Foundation IRCCS, Rome, Italy.
  • Gary Donohoe
    School of Psychology, NUI Galway, Galway, Ireland.
  • Peter Kochunov
    Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore.
  • Pedro G P Rosa
    Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
  • Anthony James
    University of Oxford, Oxford, United Kingdom.
  • Udo Dannlowski
    Department of Psychiatry and Psychotherapy, University of Münster, Germany.
  • Bernhard T Baune
    Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide.
  • André Aleman
    Interdisciplinary Center Psychopathology and Emotion regulation (ICPE), Neuroimaging Center (BCN-NIC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
  • Ian H Gotlib
    Department of Psychology, Stanford University, Stanford, CA, USA.
  • Henrik Walter
    Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, CCM, Berlin, German.
  • Martin Walter
    Clinical Affective Neuroimaging Laboratory, Leibniz Institute for Neurobiology, Magdeburg, Germany.
  • Jair C Soares
    University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Stefan Ehrlich
    Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, Germany.
  • Ruben C Gur
    Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
  • N Trung Doan
    CoE NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
  • Ingrid Agartz
    CoE NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
  • Lars T Westlye
    CoE NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
  • Fabienne Harrisberger
    Department of Psychiatry, University of Basel, Basel, Switzerland.
  • Anita Riecher-Rössler
    Department of Psychiatry, University of Basel, Basel, Switzerland.
  • Anne Uhlmann
    MRC Unit on Risk & Resilience to Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
  • Dan J Stein
    MRC Unit on Risk & Resilience to Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
  • Erin W Dickie
    Centre for Addiction and Mental Health, Toronto, Canada.
  • Edith Pomarol-Clotet
    FIDMAG Germanes Hospitalaries Research Foundation, Barcelona, Spain.
  • Paola Fuentes-Claramonte
    FIDMAG Germanes Hospitalaries Research Foundation, Barcelona, Spain.
  • Erick Jorge Canales-Rodríguez
    FIDMAG Germanes Hospitalaries Research Foundation, Barcelona, Spain.
  • Raymond Salvador
    FIDMAG Germanes Hospitalaries Research Foundation, Barcelona, Spain.
  • Alexander J Huang
    Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA.
  • Roberto Roiz-Santiañez
    University Hospital Marqués de Valdecilla, IDIVAL, Department of Psychiatry, School of Medicine, University of Cantabria, Santander, Spain.
  • Shan Cong
    Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.
  • Alexander Tomyshev
    Mental Health Research Center, Moscow, Russia.
  • Fabrizio Piras
    Laboratory of Neuropsychiatry, Santa Lucia Foundation IRCCS, Rome, Italy.
  • Daniela Vecchio
    Laboratory of Neuropsychiatry, Santa Lucia Foundation IRCCS, Rome, Italy.
  • Nerisa Banaj
    Laboratory of Neuropsychiatry, Santa Lucia Foundation IRCCS, Rome, Italy.
  • Valentina Ciullo
    Laboratory of Neuropsychiatry, Santa Lucia Foundation IRCCS, Rome, Italy.
  • Elliot Hong
    Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore.
  • Geraldo Busatto
    Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
  • Marcus V Zanetti
    Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
  • Mauricio H Serpa
    Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
  • Simon Cervenka
    Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
  • Sinead Kelly
    Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
  • Dominik Grotegerd
    Department of Psychiatry and Psychotherapy, University of Münster, Germany.
  • Matthew D Sacchet
    Department of Psychology, Stanford University, Stanford, CA, USA.
  • Ilya M Veer
    Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, CCM, Berlin, German.
  • Meng Li
    Co-Innovation Center for the Sustainable Forestry in Southern China; Cerasus Research Center; College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
  • Mon-Ju Wu
    University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Benson Irungu
    University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Esther Walton
    Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, Germany.
  • Paul M Thompson
    Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

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