title: Brain extraction using the watershed transform from markers.
abstract: Isolation of the brain from other tissue types in magnetic resonance (MR) images is an important step in many types of neuro-imaging research using both humans and animal subjects. The importance of brain extraction is well appreciated-numerous approaches have been published and the benefits of good extraction methods to subsequent processing are well known. We describe a tool-the marker based watershed scalper (MBWSS)-for isolating the brain in T1-weighted MR images built using filtering and segmentation components from the Insight Toolkit (ITK) framework. The key elements of MBWSS-the watershed transform from markers and aggressive filtering with large kernels-are techniques that have rarely been used in neuroimaging segmentation applications. MBWSS is able to reliably isolate the brain without expensive preprocessing steps, such as registration to an atlas, and is therefore useful as the first stage of processing pipelines. It is an informative example of the level of accuracy achievable without using priors in the form of atlases, shape models or libraries of examples. We validate the MBWSS using a publicly available dataset, a paediatric cohort, an adolescent cohort, intra-surgical scans and demonstrate flexibility of the approach by modifying the method to extract macaque brains.
authors.affiliation: Developmental Imaging, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Stroke and Aging Research Group, Department of Medicine, Southern Clinical School, Monash University Melbourne, VIC, Australia.
authors.forename: Richard
authors.initials: R
authors.lastname: Beare
authors.affiliation: Developmental Imaging, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Stroke and Aging Research Group, Department of Medicine, Southern Clinical School, Monash University Melbourne, VIC, Australia.
authors.forename: Jian
authors.initials: J
authors.lastname: Chen
authors.affiliation: Developmental Imaging, Murdoch Childrens Research Institute Melbourne, VIC, Australia.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Adamson
authors.affiliation: Developmental Imaging, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Department of Paediatrics, University of Melbourne VIC, Australia.
authors.forename: Timothy
authors.initials: T
authors.lastname: Silk
authors.affiliation: Developmental Imaging, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Victorian Infant Brain Studies, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Florey Department of Neuroscience and Mental Health, University of Melbourne VIC, Australia.
authors.forename: Deanne K
authors.initials: DK
authors.lastname: Thompson
authors.affiliation: Developmental Imaging, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Department of Neurosurgery, Royal Childrens Hospital Melbourne, VIC, Australia.
authors.forename: Joseph Y M
authors.initials: JY
authors.lastname: Yang
authors.affiliation: Clinical Sciences, Murdoch Childrens Research Institute Melbourne, VIC, Australia.
authors.forename: Vicki A
authors.initials: VA
authors.lastname: Anderson
authors.affiliation: Developmental Imaging, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Department of Paediatrics, University of Melbourne VIC, Australia.
authors.forename: Marc L
authors.initials: ML
authors.lastname: Seal
authors.affiliation: School of Psychology, University of Birmingham Edgbaston, UK.
authors.forename: Amanda G
authors.initials: AG
authors.lastname: Wood
keywords: Insight Toolkit; brain extraction; human brain extraction; macaque brain extraction; mathematical morphology; scalping; watershed transform from markers