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

Fidel Alfaro-Almagro; Mark Jenkinson; Neal K Bangerter; Jesper L R Andersson; Ludovica Griffanti; Gwenaëlle Douaud; Stamatios N Sotiropoulos; Saad Jbabdi; Moises Hernandez-Fernandez; Emmanuel Vallee; Diego Vidaurre; Matthew Webster; Paul McCarthy; Christopher Rorden; Alessandro Daducci; Daniel C Alexander; Hui Zhang; Iulius Dragonu; Paul M Matthews; Karla L Miller; Stephen M Smith

doi:10.1016/j.neuroimage.2017.10.034

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

Neuroimage. 2018 Feb 1:166:400-424. doi: 10.1016/j.neuroimage.2017.10.034. Epub 2017 Oct 24.

Authors

Fidel Alfaro-Almagro¹, Mark Jenkinson², Neal K Bangerter³, Jesper L R Andersson², Ludovica Griffanti², Gwenaëlle Douaud², Stamatios N Sotiropoulos⁴, Saad Jbabdi², Moises Hernandez-Fernandez², Emmanuel Vallee², Diego Vidaurre⁵, Matthew Webster², Paul McCarthy², Christopher Rorden⁶, Alessandro Daducci⁷, Daniel C Alexander⁸, Hui Zhang⁸, Iulius Dragonu⁹, Paul M Matthews¹⁰, Karla L Miller², Stephen M Smith²

Affiliations

¹ Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK. Electronic address: falmagro@fmrib.ox.ac.uk.
² Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
³ Electrical and Computer Engineering, Brigham Young University, UT, USA.
⁴ 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.
⁵ Oxford Centre for Human Brain Activity, Wellcome Centre for Integrative Neuroimaging, Department of Psychiatry, University of Oxford, UK.
⁶ Department of Psychology and McCausland Center for Brain Imaging, University of South Carolina, SC, USA.
⁷ Computer Science Department, University of Verona, Italy; Radiology Department, University Hospital Center, Switzerland.
⁸ Centre for Medical Image Computing, Department of Computer Science, University College London, UK.
⁹ Siemens Healthcare, Surrey, UK.
¹⁰ Division of Brain Sciences, Imperial College, London, UK; UK Dementia Research Institute, London, UK.

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.

Keywords: Big data imaging; Epidemiological studies; Image analysis pipeline; Machine learning; Multi-modal data integration; Quality control.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brain / diagnostic imaging*
Databases, Factual* / standards
Datasets as Topic* / standards
Humans
Image Processing, Computer-Assisted / methods*
Image Processing, Computer-Assisted / standards
Machine Learning* / standards
Magnetic Resonance Imaging / methods*
Magnetic Resonance Imaging / standards
Neuroimaging / methods*
Neuroimaging / standards
Quality Control*
United Kingdom

Abstract

Publication types

MeSH terms

Grants and funding