Abstract #3249

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

Jacob Daniel Kirstejn Hansen¹, François Lauze¹, Sune Darkner¹, Kristian Nygaard Mortensen², Simon Sanggaard², Helene Benveniste³, and Maiken Nedergaard^2,4

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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