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

• Published in: NeuroImage (Orlando, Fla.) Vol. 166; pp. 400 - 424
• Main Authors: Alfaro-Almagro, Fidel, Jenkinson, Mark, Bangerter, Neal K., Andersson, Jesper L.R., Griffanti, Ludovica, Douaud, Gwenaëlle, Sotiropoulos, Stamatios N., Jbabdi, Saad, Hernandez-Fernandez, Moises, Vallee, Emmanuel, Vidaurre, Diego, Webster, Matthew, McCarthy, Paul, Rorden, Christopher, Daducci, Alessandro, Alexander, Daniel C., Zhang, Hui, Dragonu, Iulius, Matthews, Paul M., Miller, Karla L., Smith, Stephen M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.02.2018; Elsevier Limited; Academic Press
• Subjects: Alzheimer's disease; Automation; Big data imaging; Biomarkers; Bone imaging; Brain - diagnostic imaging; Brain mapping; Brain research; Databases, Factual - standards; Datasets; Datasets as Topic - standards; Epidemiological studies; Epidemiology; Functional magnetic resonance imaging; Humans; Image analysis pipeline; Image processing; Image Processing, Computer-Assisted - methods; Image Processing, Computer-Assisted - standards; Machine learning; Machine Learning - standards; Magnetic Resonance Imaging - methods; Magnetic Resonance Imaging - standards; Medical imaging; Multi-modal data integration; Neuroimaging; Neuroimaging - methods; Neuroimaging - standards; NMR; Nuclear magnetic resonance; Quality Control; Software; Ultrasound; United Kingdom; United Kingdom > UK; Epidemiological studies; Big data imaging; Image analysis pipeline; Multi-modal data integration; Quality control; Machine learning
• ISSN: 1053-8119; 1095-9572; 1095-9572
• DOI: 10.1016/j.neuroimage.2017.10.034

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.