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Accurate ventricular volume measurements are the primary indicators of normal/abnor- mal cardiac function and are dependent on the Cardiac Magnetic Resonance (CMR) volumes being complete. However, missing or unusable slices owing to the presence of image artefacts such as respiratory or motion ghosting, aliasing, ringing and signal loss in CMR sequences, significantly hinder accuracy of anatomical and functional cardiac quantification, and recovering from those is insufficiently addressed in population imaging. In this work, we propose a new robust approach, coined Image Imputation Generative Adversarial Network (I2-GAN), to learn key features of cardiac short axis (SAX) slices near missing information, and use them as conditional variables to infer missing slices in the query volumes. In I2-GAN, the slices are first mapped to latent vectors with position features through a regression net. The latent vector corresponding to the desired position is then projected onto the slice manifold, conditioned on intensity features through a generator net. The generator comprises residual blocks with normalisation layers that are modulated with auxiliary slice information, enabling propagation of fine details through the network. In addition, a multi-scale discriminator was implemented, along with a discriminator-based feature matching loss, to further enhance performance and encourage the synthesis of visually realistic slices. Experimental results show that our method achieves significant improvements over the state-of-the-art, in missing slice imputation for CMR, with an average SSIM of 0.872. Linear regression analysis yields good agreement between reference and imputed CMR images for all cardiac measurements, with correlation coefficients of 0.991 for left ventricular volume, 0.977 for left ventricular mass and 0.961 for right ventricular volume., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020. Published by Elsevier B.V.)

• In this work, 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 • To the best of our knowledge, this is the first work that uses such an approach for patient-specific cardiac shape generation • 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, in total 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 [Display omitted] 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. [ABSTRACT FROM AUTHOR]