Automatic 3D+t four-chamber CMR quantification of the UK biobank: integrating imaging and non-imaging data priors at scale

Yan Xia, Xiang Chen, Nishant Ravikumar, Christopher Kelly, Rahman Attar, Nay Aung, Stefan Neubauer, Steffen E. Petersen, Alejandro F. Frangi

Research output: Contribution to journalArticlepeer-review


Accurate 3D modelling of cardiac chambers is essential for clinical assessment of cardiac volume and function, including structural, and motion analysis. Furthermore, to study the correlation between cardiac morphology and other patient information within a large population, it is necessary to automatically generate cardiac mesh models of each subject within the population. In this study, we introduce MCSI-Net (Multi-Cue Shape Inference Network), where we embed a statistical shape model inside a convolutional neural network and leverage both phenotypic and demographic information from the cohort to infer subject-specific reconstructions of all four cardiac chambers in 3D. In this way, we leverage the ability of the network to learn the appearance of cardiac chambers in cine cardiac magnetic resonance (CMR) images, and generate plausible 3D cardiac shapes, by constraining the prediction using a shape prior, in the form of the statistical modes of shape variation learned a priori from a subset of the population. This, in turn, enables the network to generalise to samples across the entire population. To the best of our knowledge, this is the first work that uses such an approach for patient-specific cardiac shape generation. MCSI-Net is capable of producing accurate 3D shapes using just a fraction (about 23% to 46%) of the available image data, which is of significant importance to the community as it supports the acceleration of CMR scan acquisitions. Cardiac MR images from the UK Biobank were used to train and validate the proposed method. We also present the results from analysing 40,000 subjects of the UK Biobank at 50 time-frames, totalling two million image volumes. Our model can generate more globally consistent heart shape than that of manual annotations in the presence of inter-slice motion and shows strong agreement with the reference ranges for cardiac structure and function across cardiac ventricles and atria.

Original languageEnglish
Article number102498
Number of pages17
JournalMedical Image Analysis
Publication statusPublished - Aug 2022


  • Cardiac functional indexes
  • Cardiac morphological analysis
  • Cardiac MR
  • Deep learning
  • Fully automatic analysis
  • Population imaging
  • Statistical shape models
  • UK Biobank


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