title: Brain Extraction Using Label Propagation and Group Agreement: Pincram.
abstract: Accurately delineating the brain on magnetic resonance (MR) images of the head is a prerequisite for many neuroimaging methods. Most existing methods exhibit disadvantages in that they are laborious, yield inconsistent results, and/or require training data to closely match the data to be processed. Here, we present pincram, an automatic, versatile method for accurately labelling the adult brain on T1-weighted 3D MR head images. The method uses an iterative refinement approach to propagate labels from multiple atlases to a given target image using image registration. At each refinement level, a consensus label is generated. At the subsequent level, the search for the brain boundary is constrained to the neighbourhood of the boundary of this consensus label. The method achieves high accuracy (Jaccard coefficient > 0.95 on typical data, corresponding to a Dice similarity coefficient of > 0.97) and performs better than many state-of-the-art methods as evidenced by independent evaluation on the Segmentation Validation Engine. Via a novel self-monitoring feature, the program generates the "success index," a scalar metadatum indicative of the accuracy of the output label. Pincram is available as open source software.
authors.affiliation: MedTech West at Sahlgrenska University Hospital, Gothenburg, Sweden; Institute of Neuroscience and Physiology, Gothenburg University, Gothenburg, Sweden; Centre for Brain Sciences, Imperial College, London, United Kingdom; The Neurodis Foundation, Lyon, France.
authors.forename: Rolf A
authors.initials: RA
authors.lastname: Heckemann
authors.affiliation: Department of Computing, Imperial College, London, United Kingdom.
authors.forename: Christian
authors.initials: C
authors.lastname: Ledig
authors.affiliation: Department of Computing, Imperial College, London, United Kingdom.
authors.forename: Katherine R
authors.initials: KR
authors.lastname: Gray
authors.affiliation: Department of Computing, Imperial College, London, United Kingdom; Imaging Sciences and Biomedical Engineering, King's College, London, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Aljabar
authors.affiliation: Department of Computing, Imperial College, London, United Kingdom.
authors.forename: Daniel
authors.initials: D
authors.lastname: Rueckert
authors.affiliation: Imaging Sciences and Biomedical Engineering, King's College, London, United Kingdom.
authors.forename: Joseph V
authors.initials: JV
authors.lastname: Hajnal
authors.affiliation: The Neurodis Foundation, Lyon, France; Imaging Sciences and Biomedical Engineering, King's College, London, United Kingdom.
authors.forename: Alexander
authors.initials: A
authors.lastname: Hammers
mesh_terms: D000328:Adult; D001921:Brain / Q000033:anatomy & histology*; D001931:Brain Mapping / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008875:Middle Aged; D012984:Software; D055815:Young Adult