Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank.

Journal: NeuroImage
Published Date: Oct 24, 2017

Abstract

UK Biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. It is currently in the process of bringing back 100,000 of the original participants for brain, heart and body MRI, carotid ultrasound and low-dose bone/fat x-ray. The brain imaging component covers 6 modalities (T1, T2 FLAIR, susceptibility weighted MRI, Resting fMRI, Task fMRI and Diffusion MRI). Raw and processed data from the first 10,000 imaged subjects has recently been released for general research access. To help convert this data into useful summary information we have developed an automated processing and QC (Quality Control) pipeline that is available for use by other researchers. In this paper we describe the pipeline in detail, following a brief overview of UK Biobank brain imaging and the acquisition protocol. We also describe several quantitative investigations carried out as part of the development of both the imaging protocol and the processing pipeline.

Authors

  • Fidel Alfaro-Almagro
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK. Electronic address: falmagro@fmrib.ox.ac.uk.
  • Mark Jenkinson
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Neal K Bangerter
    Electrical and Computer Engineering, Brigham Young University, UT, USA.
  • Jesper L R Andersson
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Ludovica Griffanti
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Gwenaëlle Douaud
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Stamatios N Sotiropoulos
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK; Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, UK.
  • Saad Jbabdi
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Moises Hernandez-Fernandez
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Emmanuel Vallee
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Diego Vidaurre
    Oxford Centre for Human Brain Activity, Wellcome Centre for Integrative Neuroimaging, Department of Psychiatry, University of Oxford, UK.
  • Matthew Webster
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Paul McCarthy
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Christopher Rorden
    McCausland Center for Brain Imaging, Department of Psychology, University of South Carolina, 915 Greene St, Columbia, SC, 29016, USA. rorden@sc.edu.
  • Alessandro Daducci
    Computer Science Department, University of Verona, Italy; Radiology Department, University Hospital Center, Switzerland.
  • Daniel C Alexander
    Centre for Medical Image Computing and Dept of Computer Science, University College London, Gower Street, London WC1E 6BT, UK.
  • Hui Zhang
    Department of Pulmonary Vessel and Thrombotic Disease, Sixth Medical Center, Chinese PLA General Hospital, Beijing, China.
  • Iulius Dragonu
    Siemens Healthcare, Surrey, UK.
  • Paul M Matthews
    Division of Brain Sciences, Imperial College London, London, UK.
  • Karla L Miller
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  • Stephen M Smith
    Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.

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