• Sebastiano Ferraris, Johannes van der Merwe, Lennart Van Der Veeken, Ferran Prados, Juan-Eugenio Iglesias, Andrew Melbourne, Marco Lorenzi, Marc Modat, Willy Gsell, Jan Deprest, and Tom Vercauteren.
• Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK. Electronic address: s.ferraris@ucl.ac.uk.
• Neuroimage. 2018 Oct 1; 179: 187-198.

AbstractThe rabbit model has become increasingly popular in neurodevelopmental studies as it is best suited to bridge the gap in translational research between small and large animals. In the context of preclinical studies, high-resolution magnetic resonance imaging (MRI) is often the best modality to investigate structural and functional variability of the brain, both in vivo and ex vivo. In most of the MRI-based studies, an important requirement to analyze the acquisitions is an accurate parcellation of the considered anatomical structures. Manual segmentation is time-consuming and typically poorly reproducible, while state-of-the-art automated segmentation algorithms rely on available atlases. In this work we introduce the first digital neonatal rabbit brain atlas consisting of 12 multi-modal acquisitions, parcellated into 89 areas according to a hierarchical taxonomy. Delineations were performed iteratively, alternating between segmentation propagation, label fusion and manual refinements, with the aim of controlling the quality while minimizing the bias introduced by the chosen sequence. Reliability and accuracy were assessed with cross-validation and intra- and inter-operator test-retests. Multi-atlas, versioned controlled segmentations repository and supplementary materials download links are available from the software repository documentation at https://github.com/gift-surg/SPOT-A-NeonatalRabbit.Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

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