Automated cardiovascular magnetic resonance image analysis with fully convolutional networks 08 Information and Computing Sciences 0801 Artificial Intelligence and Image Processing

Wenjia Bai, Matthew Sinclair, Giacomo Tarroni, Ozan Oktay, Martin Rajchl, Ghislain Vaillant, Aaron M. Lee, Nay Aung, Elena Lukaschuk, Mihir M. Sanghvi, Filip Zemrak, Kenneth Fung, Jose Miguel Paiva, Valentina Carapella, Young Jin Kim, Hideaki Suzuki, Bernhard Kainz, Paul M. Matthews, Steffen E. Petersen, Stefan K. PiechnikStefan Neubauer, Ben Glocker, Daniel Rueckert

Research output: Contribution to journalArticlepeer-review

336 Citations (Scopus)


Background: Cardiovascular resonance (CMR) imaging is a standard imaging modality for assessing cardiovascular diseases (CVDs), the leading cause of death globally. CMR enables accurate quantification of the cardiac chamber volume, ejection fraction and myocardial mass, providing information for diagnosis and monitoring of CVDs. However, for years, clinicians have been relying on manual approaches for CMR image analysis, which is time consuming and prone to subjective errors. It is a major clinical challenge to automatically derive quantitative and clinically relevant information from CMR images. Methods: Deep neural networks have shown a great potential in image pattern recognition and segmentation for a variety of tasks. Here we demonstrate an automated analysis method for CMR images, which is based on a fully convolutional network (FCN). The network is trained and evaluated on a large-scale dataset from the UK Biobank, consisting of 4,875 subjects with 93,500 pixelwise annotated images. The performance of the method has been evaluated using a number of technical metrics, including the Dice metric, mean contour distance and Hausdorff distance, as well as clinically relevant measures, including left ventricle (LV) end-diastolic volume (LVEDV) and end-systolic volume (LVESV), LV mass (LVM); right ventricle (RV) end-diastolic volume (RVEDV) and end-systolic volume (RVESV). Results: By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images. On a short-axis image test set of 600 subjects, it achieves an average Dice metric of 0.94 for the LV cavity, 0.88 for the LV myocardium and 0.90 for the RV cavity. The mean absolute difference between automated measurement and manual measurement is 6.1 mL for LVEDV, 5.3 mL for LVESV, 6.9 gram for LVM, 8.5 mL for RVEDV and 7.2 mL for RVESV. On long-axis image test sets, the average Dice metric is 0.93 for the LA cavity (2-chamber view), 0.95 for the LA cavity (4-chamber view) and 0.96 for the RA cavity (4-chamber view). The performance is comparable to human inter-observer variability. Conclusions: We show that an automated method achieves a performance on par with human experts in analysing CMR images and deriving clinically relevant measures.

Original languageEnglish
Article number65
JournalJournal of Cardiovascular Magnetic Resonance
Issue number1
Publication statusPublished - 2018 Sept 14

Bibliographical note

Funding Information:
This work is supported by the SmartHeart EPSRC Programme Grant (EP/P001009/1). G.T. is supported by a Marie Skłodowska Curie European Fellowship. A.L. and S.E.P. acknowledge support from the NIHR Barts Biomedical Research Centre and from the MRC for the MRC eMedLab Medical Bioinformatics infrastructure (MR/L016311/1), which enables data access. N.A. is supported by a Wellcome Trust Research Training Fellowship (203553/Z/Z). S.N. and S.K.P. acknowledge support from the NIHR Oxford Biomedical Research Centre and the Oxford BHF Centre of Research Excellence. S.E.P., S.K.P. and S.N. acknowledge the British Heart Foundation (BHF) for funding the manual analysis to create a cardiovascular magnetic resonance imaging reference standard for the UK Biobank imaging resource in 5000 CMR scans (PG/14/89/31194). H.S. is supported by a Research Fellowship from the Uehara Memorial Foundation. P.M.M. gratefully acknowledges support from the Edmond J. Safra Foundation and Lily Safra, the Imperial College Healthcare Trust Biomedical Research Centre, the EPSRC Centre for Mathematics in Precision Healthcare and the MRC.

Publisher Copyright:
© 2018 The Author(s).

All Science Journal Classification (ASJC) codes

  • Radiological and Ultrasound Technology
  • Radiology Nuclear Medicine and imaging
  • Cardiology and Cardiovascular Medicine


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