title: Derivation of high-resolution MRI atlases of the human cerebellum at 3T and segmentation using multiple automatically generated templates.
abstract: The cerebellum has classically been linked to motor learning and coordination. However, there is renewed interest in the role of the cerebellum in non-motor functions such as cognition and in the context of different neuropsychiatric disorders. The contribution of neuroimaging studies to advancing understanding of cerebellar structure and function has been limited, partly due to the cerebellum being understudied as a result of contrast and resolution limitations of standard structural magnetic resonance images (MRI). These limitations inhibit proper visualization of the highly compact and detailed cerebellar foliations. In addition, there is a lack of robust algorithms that automatically and reliably identify the cerebellum and its subregions, further complicating the design of large-scale studies of the cerebellum. As such, automated segmentation of the cerebellar lobules would allow detailed population studies of the cerebellum and its subregions. In this manuscript, we describe a novel set of high-resolution in vivo atlases of the cerebellum developed by pairing MR imaging with a carefully validated manual segmentation protocol. Using these cerebellar atlases as inputs, we validate a novel automated segmentation algorithm that takes advantage of the neuroanatomical variability that exists in a given population under study in order to automatically identify the cerebellum, and its lobules. Our automatic segmentation results demonstrate good accuracy in the identification of all lobules (mean Kappa [κ]=0.731; range 0.40-0.89), and the entire cerebellum (mean κ=0.925; range 0.90-0.94) when compared to "gold-standard" manual segmentations. These results compare favorably in comparison to other publically available methods for automatic segmentation of the cerebellum. The completed cerebellar atlases are available freely online (http://imaging-genetics.camh.ca/cerebellum) and can be customized to the unique neuroanatomy of different subjects using the proposed segmentation pipeline (https://github.com/pipitone/MAGeTbrain).
authors.affiliation: Kimel Family Translational Imaging Genetics Research Laboratory, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada. Electronic address: mtpark89@gmail.com.
authors.forename: Min Tae M
authors.initials: MT
authors.lastname: Park
authors.affiliation: Kimel Family Translational Imaging Genetics Research Laboratory, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada.
authors.forename: Jon
authors.initials: J
authors.lastname: Pipitone
authors.affiliation: Department of Psychology, Concordia University, Montreal, QC, Canada.
authors.forename: Lawrence H
authors.initials: LH
authors.lastname: Baer
authors.affiliation: Kimel Family Translational Imaging Genetics Research Laboratory, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada.
authors.forename: Julie L
authors.initials: JL
authors.lastname: Winterburn
authors.affiliation: Kimel Family Translational Imaging Genetics Research Laboratory, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada.
authors.forename: Yashvi
authors.initials: Y
authors.lastname: Shah
authors.affiliation: MRI Unit, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada.
authors.forename: Sofia
authors.initials: S
authors.lastname: Chavez
authors.affiliation: School of Psychology, University of Wollongong, Wollongong, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Schira
authors.affiliation: MRI Unit, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada; Division of Neurology, Department of Medicine, University of Toronto, Toronto, Canada.
authors.forename: Nancy J
authors.initials: NJ
authors.lastname: Lobaugh
authors.affiliation: Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada.
authors.forename: Jason P
authors.initials: JP
authors.lastname: Lerch
authors.affiliation: Kimel Family Translational Imaging Genetics Research Laboratory, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada.
authors.forename: Aristotle N
authors.initials: AN
authors.lastname: Voineskos
authors.affiliation: Kimel Family Translational Imaging Genetics Research Laboratory, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada. Electronic address: mallar.chakravarty@camh.ca.
authors.forename: M Mallar
authors.initials: MM
authors.lastname: Chakravarty
mesh_terms: D000328:Adult; D000465:Algorithms; D000716:Anatomy, Artistic / Q000379:methods; D001271:Atlases as Topic; D001931:Brain Mapping; D002531:Cerebellum / Q000033:anatomy & histology*; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male
keywords: Atlas; Automatic; Cerebellum; High resolution; Lobule; MRI