title: A multi-atlas based method for automated anatomical rat brain MRI segmentation and extraction of PET activity.
abstract: BACKGROUND
  Preclinical in vivo imaging requires precise and reproducible delineation of brain structures. Manual segmentation is time consuming and operator dependent. Automated segmentation as usually performed via single atlas registration fails to account for anatomo-physiological variability. We present, evaluate, and make available a multi-atlas approach for automatically segmenting rat brain MRI and extracting PET activies.
  
  
  METHODS
  High-resolution 7T 2DT2 MR images of 12 Sprague-Dawley rat brains were manually segmented into 27-VOI label volumes using detailed protocols. Automated methods were developed with 7/12 atlas datasets, i.e. the MRIs and their associated label volumes. MRIs were registered to a common space, where an MRI template and a maximum probability atlas were created. Three automated methods were tested: 1/registering individual MRIs to the template, and using a single atlas (SA), 2/using the maximum probability atlas (MP), and 3/registering the MRIs from the multi-atlas dataset to an individual MRI, propagating the label volumes and fusing them in individual MRI space (propagation & fusion, PF). Evaluation was performed on the five remaining rats which additionally underwent [18F]FDG PET. Automated and manual segmentations were compared for morphometric performance (assessed by comparing volume bias and Dice overlap index) and functional performance (evaluated by comparing extracted PET measures).
  
  
  RESULTS
  Only the SA method showed volume bias. Dice indices were significantly different between methods (PF>MP>SA). PET regional measures were more accurate with multi-atlas methods than with SA method.
  
  
  CONCLUSIONS
  Multi-atlas methods outperform SA for automated anatomical brain segmentation and PET measure's extraction. They perform comparably to manual segmentation for FDG-PET quantification. Multi-atlas methods are suitable for rapid reproducible VOI analyses.
authors.affiliation: Université Claude Bernard Lyon, INSERM, CNRS, Lyon Neuroscience Research Center, Radiopharmaceutical and Neurochemical Biomarkers Team, Lyon, France; Hospices Civils de Lyon, Lyon, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Lancelot
authors.affiliation: CERMEP - Imagerie du Vivant, Lyon, France.
authors.forename: Roxane
authors.initials: R
authors.lastname: Roche
authors.affiliation: CERMEP - Imagerie du Vivant, Lyon, France.
authors.forename: Afifa
authors.initials: A
authors.lastname: Slimen
authors.affiliation: CERMEP - Imagerie du Vivant, Lyon, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Bouillot
authors.affiliation: Université Claude Bernard Lyon, INSERM, CNRS, Lyon Neuroscience Research Center, Radiopharmaceutical and Neurochemical Biomarkers Team, Lyon, France; Hospices Civils de Lyon, Lyon, France.
authors.forename: Elise
authors.initials: E
authors.lastname: Levigoureux
authors.affiliation: CERMEP - Imagerie du Vivant, Lyon, France.
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Langlois
authors.affiliation: Université Claude Bernard Lyon, INSERM, CNRS, Lyon Neuroscience Research Center, Radiopharmaceutical and Neurochemical Biomarkers Team, Lyon, France; Hospices Civils de Lyon, Lyon, France; CERMEP - Imagerie du Vivant, Lyon, France.
authors.forename: Luc
authors.initials: L
authors.lastname: Zimmer
authors.affiliation: CERMEP - Imagerie du Vivant, Lyon, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Costes
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology / Q000000981:diagnostic imaging* / Q000502:physiology; D001931:Brain Mapping / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods; D049268:Positron-Emission Tomography / Q000379:methods*; D051381:Rats; D017207:Rats, Sprague-Dawley; D012680:Sensitivity and Specificity