Automatic structural parcellation of mouse brain MRI using multi-atlas label fusion.
Multi-atlas segmentation propagation has evolved quickly in recent years, becoming a state-of-the-art methodology for automatic parcellation of structural images. However, few studies have applied these methods to preclinical research. In this study, we present a fully automatic framework for mouse brain MRI structural parcellation using multi-atlas segmentation propagation. The framework adopts the similarity and truth estimation for propagated segmentations (STEPS) algorithm, which utilises a locally normalised cross correlation similarity metric for atlas selection and an extended simultaneous truth and performance level estimation (STAPLE) framework for multi-label fusion. The segmentation accuracy of the multi-atlas framework was evaluated using publicly available mouse brain atlas databases with pre-segmented manually labelled anatomical structures as the gold standard, and optimised parameters were obtained for the STEPS algorithm in the label fusion to achieve the best segmentation accuracy. We showed that our multi-atlas framework resulted in significantly higher segmentation accuracy compared to single-atlas based segmentation, as well as to the original STAPLE framework.
Centre for Medical Imaging Computing, University College London, London, England, United Kingdom ; Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom.
Da
D
Ma
Centre for Medical Imaging Computing, University College London, London, England, United Kingdom.
Manuel J
MJ
Cardoso
Centre for Medical Imaging Computing, University College London, London, England, United Kingdom.
Marc
M
Modat
Centre for Medical Imaging Computing, University College London, London, England, United Kingdom ; Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom.
Nick
N
Powell
Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom.
Jack
J
Wells
Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom.
Holly
H
Holmes
Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, England, United Kingdom.
Frances
F
Wiseman
Division of Immune Cell Biology, MRC National Institute for Medical Research, London, England, United Kingdom.
Victor
V
Tybulewicz
Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, England, United Kingdom.
Elizabeth
E
Fisher
Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom.
Mark F
MF
Lythgoe
Centre for Medical Imaging Computing, University College London, London, England, United Kingdom.
Sébastien
S
Ourselin
D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000648:ultrastructure*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D051379:Mice; D008822:Mice, Transgenic