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

TLDR

UK Biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. This paper describes an automated processing and QC pipeline that converts UK Biobank brain imaging data into usable summary information. The pipeline processes six brain imaging modalities (T1, T2 FLAIR, SWI, resting fMRI, task fMRI, and diffusion MRI) and incorporates quantitative investigations to refine the imaging protocol and processing steps. The first 10,000 imaged subjects’ raw and processed data have been released for general research access.

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.