title: Automatic segmentation of the striatum and globus pallidus using MIST: Multimodal Image Segmentation Tool.
abstract: Accurate segmentation of the subcortical structures is frequently required in neuroimaging studies. Most existing methods use only a T1-weighted MRI volume to segment all supported structures and usually rely on a database of training data. We propose a new method that can use multiple image modalities simultaneously and a single reference segmentation for initialisation, without the need for a manually labelled training set. The method models intensity profiles in multiple images around the boundaries of the structure after nonlinear registration. It is trained using a set of unlabelled training data, which may be the same images that are to be segmented, and it can automatically infer the location of the physical boundary using user-specified priors. We show that the method produces high-quality segmentations of the striatum, which is clearly visible on T1-weighted scans, and the globus pallidus, which has poor contrast on such scans. The method compares favourably to existing methods, showing greater overlap with manual segmentations and better consistency.
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: FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
authors.forename: Gwenaëlle
authors.initials: G
authors.lastname: Douaud
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), MIRCen, F-92260 Fontenay-aux-Roses, France; Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, F-92260 Fontenay-aux-Roses, France.
authors.forename: Veronique
authors.initials: V
authors.lastname: Gaura
authors.affiliation: AP-HP, Hôpital Henri Mondor, Centre de Référence-Maladie de Huntington, Neurologie cognitive, Créteil, France; Université Paris Est, Faculté de médecine, Créteil, France; INSERM U955, Equipe 01, Neuropsychologie Interventionnelle, Créteil, France; Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL Research University, Paris, France.
authors.forename: Anne-Catherine
authors.initials: AC
authors.lastname: Bachoud-Levi
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département des Sciences du Vivant (DSV), Institut d'Imagerie Biomédicale (I2BM), MIRCen, F-92260 Fontenay-aux-Roses, France; Centre Expert Parkinson et NEURATRIS, CHU Henri Mondor, Pôle Neuro-Locomoteur, Assistance Publique Hôpitaux de Paris et Université Paris Est Créteil, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Remy
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; D000465:Algorithms; D001931:Brain Mapping / Q000379:methods*; D003342:Corpus Striatum / Q000033:anatomy & histology*; D005260:Female; D005917:Globus Pallidus / Q000033:anatomy & histology*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D008279:Magnetic Resonance Imaging / Q000379:methods; D008297:Male; D008959:Models, Neurological; D038361:Neuronavigation / Q000379:methods; D010363:Pattern Recognition, Automated / Q000379:methods
keywords: Brain; Globus pallidus; Huntington; Multimodal; Segmentation; Striatum