title: Automated segmentation of the substantia nigra, subthalamic nucleus and red nucleus in 7T data at young and old age.
abstract: With recent developments in MR acquisition at 7T, smaller brainstem structures such as the red nuclei, substantia nigra and subthalamic nuclei can be imaged with good contrast and resolution. These structures have important roles both in the study of the healthy brain and in diseases such as Parkinson's disease, but few methods have been described to automatically segment them. In this paper, we extend a method that we have previously proposed for segmentation of the striatum and globus pallidus to segment these deeper and smaller structures. We modify the method to allow more direct control over segmentation smoothness by using a Markov random field prior. We investigate segmentation performance in three age groups and show that the method produces consistent results that correspond well with manual segmentations. We perform a vertex-based analysis to identify changes with age in the shape of the structures and present results suggesting that the method may be at least as effective as manual delineation in capturing differences between subjects.
authors.affiliation: FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom. Electronic address: eelke.visser@ndcn.ox.ac.uk.
authors.forename: Eelke
authors.initials: E
authors.lastname: Visser
authors.affiliation: Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, Netherlands.
authors.forename: Max C
authors.initials: MC
authors.lastname: Keuken
authors.affiliation: Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, Netherlands.
authors.forename: Birte U
authors.initials: BU
authors.lastname: Forstmann
authors.affiliation: FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
authors.forename: Mark
authors.initials: M
authors.lastname: Jenkinson
mesh_terms: D000328:Adult; D000368:Aged; D001931:Brain Mapping / Q000379:methods*; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008279:Magnetic Resonance Imaging; D008297:Male; D008875:Middle Aged; D010363:Pattern Recognition, Automated; D012012:Red Nucleus / Q000033:anatomy & histology*; D012815:Signal Processing, Computer-Assisted; D013378:Substantia Nigra / Q000033:anatomy & histology*; D020531:Subthalamic Nucleus / Q000033:anatomy & histology*; D055815:Young Adult