title: An automatic rat brain extraction method based on a deformable surface model.
abstract: The extraction of the brain from the skull in medical images is a necessary first step before image registration or segmentation. While pre-clinical MR imaging studies on small animals, such as rats, are increasing, fully automatic imaging processing techniques specific to small animal studies remain lacking. In this paper, we present an automatic rat brain extraction method, the Rat Brain Deformable model method (RBD), which adapts the popular human brain extraction tool (BET) through the incorporation of information on the brain geometry and MR image characteristics of the rat brain. The robustness of the method was demonstrated on T2-weighted MR images of 64 rats and compared with other brain extraction methods (BET, PCNN, PCNN-3D). The results demonstrate that RBD reliably extracts the rat brain with high accuracy (>92% volume overlap) and is robust against signal inhomogeneity in the images.
authors.affiliation: Department of Electrical and Computer Engineering, George Washington University, Washington, DC 20052, USA.
authors.forename: Jiehua
authors.initials: J
authors.lastname: Li
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Liu
authors.forename: Jiachen
authors.initials: J
authors.lastname: Zhuo
authors.forename: Rao P
authors.initials: RP
authors.lastname: Gullapalli
authors.forename: Jason M
authors.initials: JM
authors.lastname: Zara
mesh_terms: D000465:Algorithms; D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008279:Magnetic Resonance Imaging; D051381:Rats
keywords: Deformable surface model; MRI; Rat brain extraction