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 & 1 others Stephen M. Smith

Research output: Contribution to journalArticle

60 Citations (Scopus)

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.

LanguageEnglish
Pages400-424
Number of pages25
JournalNeuroImage
Volume166
DOIs
Publication statusPublished - 1 Feb 2018

Keywords

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

ASJC Scopus subject areas

  • Neurology
  • Cognitive Neuroscience

Cite this

Alfaro-Almagro, F., Jenkinson, M., Bangerter, N. K., Andersson, J. L. R., Griffanti, L., Douaud, G., ... Smith, S. M. (2018). Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank. NeuroImage, 166, 400-424. https://doi.org/10.1016/j.neuroimage.2017.10.034
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. / Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank. In: NeuroImage. 2018 ; Vol. 166. pp. 400-424.
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Alfaro-Almagro, F, Jenkinson, M, Bangerter, NK, Andersson, JLR, Griffanti, L, Douaud, G, Sotiropoulos, SN, Jbabdi, S, Hernandez-Fernandez, M, Vallee, E, Vidaurre, D, Webster, M, McCarthy, P, Rorden, C, Daducci, A, Alexander, DC, Zhang, H, Dragonu, I, Matthews, PM, Miller, KL & Smith, SM 2018, 'Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank', NeuroImage, vol. 166, pp. 400-424. https://doi.org/10.1016/j.neuroimage.2017.10.034

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

In: NeuroImage, Vol. 166, 01.02.2018, p. 400-424.

Research output: Contribution to journalArticle

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AU - McCarthy, Paul

AU - Rorden, Christopher

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