title: Automatic method for tracing regions of interest in rat brain magnetic resonance imaging studies.
abstract: OBJECTIVE
  To automatically extract regions of interest (ROIs) and simultaneously preserve the anatomical characteristics of each individual, we developed a new atlas-based method utilizing a pair of coregistered brain template and digital atlas.
  
  
  METHODS
  Unlike the previous atlas-based method, this method treats each individual as the target image, and the template and atlas are each transformed to register with the individual. To evaluate the accuracy of this method we implemented it in extracting the hippocampus from two groups of T(2)-weighted structural images with different spatial resolutions and a group of T(2)*-weighted functional images. Furthermore, the results were compared against a manually segmented hippocampus and an atlas-derived hippocampus.
  
  
  RESULTS
  Jaccard similarity (JS) reached 84.7%-90.5%, and relative error in volume (RV) was 4.8%-12.7%. The consistency observed between the results of the proposed method and manual drawing was therefore considerable.
  
  
  CONCLUSIONS
  We developed a new atlas-based method for ROI extraction that can automatically extract ROI and simultaneously preserve each individual's unique anatomical characteristics.
authors.affiliation: Physical Science and Technology College, Zhengzhou University, Zhengzhou, China.
authors.forename: Binbin
authors.initials: B
authors.lastname: Nie
authors.forename: Jiaojie
authors.initials: J
authors.lastname: Hui
authors.forename: Lijing
authors.initials: L
authors.lastname: Wang
authors.forename: Pei
authors.initials: P
authors.lastname: Chai
authors.forename: Juan
authors.initials: J
authors.lastname: Gao
authors.forename: Shuangquan
authors.initials: S
authors.lastname: Liu
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Zhang
authors.forename: Baoci
authors.initials: B
authors.lastname: Shan
authors.forename: Shujun
authors.initials: S
authors.lastname: Zhao
mesh_terms: D000818:Animals; D001921:Brain / Q000473:pathology*; D001931:Brain Mapping / Q000379:methods / Q000592:standards*; D001330:Electronic Data Processing; D005260:Female; D006624:Hippocampus / Q000473:pathology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods* / Q000592:standards*; D008297:Male; D008953:Models, Anatomic; D010363:Pattern Recognition, Automated; D051381:Rats; D017207:Rats, Sprague-Dawley; D015203:Reproducibility of Results