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MRI Whole Heart Segmentation Using Discrete Nonlinear Registration and Fast Non-local Fusion

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Statistical Atlases and Computational Models of the Heart. ACDC and MMWHS Challenges (STACOM 2017)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 10663))

Abstract

We present a robust and accurate method for multi-atlas segmentation of whole heart MRI scans. After preprocessing, which includes resampling to isotropic voxel sizes and cropping or padding to same dimensions, all training scans are registered linearly and nonlinearly to an unseen set of test scans. We employ the efficient discrete registration framework called deeds that captures large shape variations across scans, performed best in a recent registration comparison on abdominal scans and requires less than 2 min of computation time per scan. Subsequently, we perform multi-atlas label fusion using a non-local means approach with a normalised SSD metric and a fast implementation using boxfilters. Subsequently, a multi-label random walk is performed on the obtained probability maps for an edge-preserving smoothing. Without performing any domain-specific parameter tuning, we obtained a Dice accuracy of 86.0% (averaged across 7 labels) and 87.0% for the whole heart on the MRI test dataset, which is the first rank of the MICCAI 2017 challenge. The segmentations are also visually very smooth using this fully automatic method.

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Acknowledgements

We would like to thank the organisers of the MM-WHS 2017 for providing this rich new dataset to the public, which enables the evaluation of new algorithms for the problem of detailed 3D heart segmentation.

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Authors and Affiliations

  1. Institute of Medical Informatics, University of Lübeck, Lübeck, Germany

    Mattias P. Heinrich

  2. IADI, U947, Inserm, CHRU de Nancy, Vandoeuvre les Nancy, France

    Julien Oster

Authors
  1. Mattias P. Heinrich
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  2. Julien Oster
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Corresponding author

Correspondence to Mattias P. Heinrich .

Editor information

Editors and Affiliations

  1. Sunnybrook Research Institute, University of Toronto, Toronto, Ontario, Canada

    Mihaela Pop

  2. Inria-Asclepios, Sophia Antipolis, France

    Maxime Sermesant

  3. Université de Sherbrooke, Quebec City, Québec, Canada

    Pierre-Marc Jodoin

  4. University Bourgogne, Dijon, France

    Alain Lalande

  5. Fudan University, Shanghai, China

    Xiahai Zhuang

  6. Cardiovascular Research Center, National Heart and Lung Institute, Royal Brompton Hospital, London, United Kingdom

    Guang Yang

  7. University of Auckland, Auckland, New Zealand

    Alistair Young

  8. CREATIS, INSA-Lyon, Villeurbanne, France

    Olivier Bernard

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Heinrich, M.P., Oster, J. (2018). MRI Whole Heart Segmentation Using Discrete Nonlinear Registration and Fast Non-local Fusion. In: Pop, M., et al. Statistical Atlases and Computational Models of the Heart. ACDC and MMWHS Challenges. STACOM 2017. Lecture Notes in Computer Science(), vol 10663. Springer, Cham. https://doi.org/10.1007/978-3-319-75541-0_25

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  • DOI: https://doi.org/10.1007/978-3-319-75541-0_25

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-75540-3

  • Online ISBN: 978-3-319-75541-0

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