Testing a deep convolutional neural network for automated hippocampus segmentation in a longitudinal sample of healthy participants.

Journal: NeuroImage
Published Date: May 7, 2019

Abstract

Subtle changes in hippocampal volumes may occur during both physiological and pathophysiological processes in the human brain. Assessing hippocampal volumes manually is a time-consuming procedure, however, creating a need for automated segmentation methods that are both fast and reliable over time. Segmentation algorithms that employ deep convolutional neural networks (CNN) have emerged as a promising solution for large longitudinal neuroimaging studies. However, for these novel algorithms to be useful in clinical studies, the accuracy and reproducibility should be established on independent datasets. Here, we evaluate the performance of a CNN-based hippocampal segmentation algorithm that was developed by Thyreau and colleagues - Hippodeep. We compared its segmentation outputs to manual segmentation and FreeSurfer 6.0 in a sample of 200 healthy participants scanned repeatedly at seven sites across Canada, as part of the Canadian Biomarker Integration Network in Depression consortium. The algorithm demonstrated high levels of stability and reproducibility of volumetric measures across all time points compared to the other two techniques. Although more rigorous testing in clinical populations is necessary, this approach holds promise as a viable option for tracking volumetric changes in longitudinal neuroimaging studies.

Authors

  • Nikita Nogovitsyn
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada; Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada. Electronic address: n.nogovitsyn@ucalgary.ca.
  • Roberto Souza
    Medical Imaging and Computing Laboratory, Department of Computer Engineering and Industrial Automation, University of Campinas, Campinas, São Paulo, Brazil; Departments of Radiology and Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada; Calgary Image Processing and Analysis Centre, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada; Seaman Family Magnetic Resonance Research Centre, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada. Electronic address: roberto.medeirosdeso@ucalgary.ca.
  • Meghan Muller
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada; Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
  • Amelia Srajer
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
  • Stefanie Hassel
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada; Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB, Canada.
  • Stephen R Arnott
    Rotman Research Institute, Baycrest, Toronto, ON, Canada.
  • Andrew D Davis
    Department of Psychology, Neuroscience & Behaviour, McMaster University, St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada.
  • Geoffrey B Hall
    Department of Psychology, Neuroscience & Behaviour, McMaster University, St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada.
  • Jacqueline K Harris
    Department of Computer Science, University of Alberta, Edmonton, AB, Canada.
  • Mojdeh Zamyadi
    Rotman Research Institute, Baycrest, Toronto, ON, Canada.
  • Paul D Metzak
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
  • Zahinoor Ismail
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada.
  • Signe L Bray
    Department of Radiology, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada; Child & Adolescent Imaging Research (CAIR) Program, Calgary, AB, Canada.
  • Catherine Lebel
    University of Calgary, Calgary, Alberta, Canada.
  • Jean M Addington
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
  • Roumen Milev
    Department of Psychiatry and Psychology, Queen's University, Providence Care Hospital, Kingston, ON, Canada.
  • Kate L Harkness
    Department of Psychology, Queen's University, Kingston, ON, Canada.
  • Benicio N Frey
    Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.
  • Raymond W Lam
    Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada.
  • Stephen C Strother
    Baycrest and Department of Medical Biophysics, Rotman Research Center, University of Toronto, Toronto, ON, Canada.
  • Benjamin I Goldstein
    Centre for Youth Bipolar Disorder, Sunnybrook Health Sciences Centre, Toronto, ON, Canada; Departments of Psychiatry and Pharmacology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
  • Susan Rotzinger
    Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
  • Sidney H Kennedy
    Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
  • Glenda M MacQueen
    Department of Psychiatry, University of Calgary, Calgary, AB, Canada.

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