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Abstract #3249

Brain extraction and segmentation framework for bias field rich cranial MRI scans of rats

Jacob Daniel Kirstejn Hansen1, Fran├žois Lauze1, Sune Darkner1, Kristian Nygaard Mortensen2, Simon Sanggaard2, Helene Benveniste3, and Maiken Nedergaard2,4

1Department of Computer Science, University of Copenhagen, Copenhagen, Denmark, 2Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark, 3Anesthesiology, Yale School of Medicine, Yale University, New Haven, CT, United States, 4Center for Translational Neuromedicine, University of Rochester, Rochester, NY, United States

This abstract presents a framework to extract brain tissue and internal Cerebrospinal fluid in cranial magnetic resonance imaging of rats with strong bias fields. Desired segments are obtained through bias field correction and several passes of segmentation. A refinement procedure is proposed to remove brain surface CSF. Promising planar and 3D visualizations of results are presented and demonstrate the capabilities of the framework.

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