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. MillerStephen M. Smith

*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

76 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)400-424
Number of pages25
Publication statusPublished - 1 Feb 2018
Externally publishedYes


  • Big data imaging
  • Epidemiological studies
  • Image analysis pipeline
  • Machine learning
  • Multi-modal data integration
  • Quality control


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