title: Two-stage multishape segmentation of brain structures using image intensity, tissue type, and location information.
abstract: OBJECTIVE
  The authors propose a fast, robust, nonparametric, entropy-based, coupled, multishape approach to segment subcortical brain structures from magnetic resonance images (MRIs).
  
  
  METHODS
  The proposed method uses three types of information: Image intensity, tissue types, and locations of structures. The image intensity information is captured by estimating the probability density function (pdf) of the image intensities in each structure. The tissue type information is captured by applying an unsupervised tissue segmentation method to the image and estimating a probability mass function (pmf) for the tissue type of each structure. The location information is captured by estimating pdf of the location of each structure from the training datasets. The resulting pmf's and pdf's are used to define an entropy function whose minimum corresponds to a desirable segmentation of the structures. The authors propose a three-step optimization strategy for the segmentation method. In the first step, a powerful automatic initialization method is developed based on tissue type and location information of the structures. In the second step, a quasi-Newton method is used to optimize the parameters of the energy function. To speed up the iterations, derivatives of the energy function with respect to its parameters are analytically derived and used in the optimization process. In the last step, the limitations related to the prior shape model are removed and a level-set method is applied for the fine tuning of the segmentation results.
  
  
  RESULTS
  The proposed method is applied to two different datasets and the results are compared to those of previous methods in literature. Experimental results are presented for lateral ventricles, caudate, thalamus, putamen, pallidum, hippocampus, and amygdala.
  
  
  CONCLUSIONS
  The results illustrate superior performance of the proposed segmentation method compared to other methods in literature. The execution time of the algorithm is a few minutes, suitable for a variety of applications.
authors.affiliation: School of Electrical and Computer Engineering, University of Tehran, Iran.
authors.forename: Alireza
authors.initials: A
authors.lastname: Akhondi-Asl
authors.forename: Hamid
authors.initials: H
authors.lastname: Soltanian-Zadeh
mesh_terms: D000465:Algorithms; D001921:Brain / Q000033:anatomy & histology*; D006801:Humans; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity