title: Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods.
abstract: Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.
authors.affiliation: MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Serag
authors.affiliation: MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK.
authors.forename: Manuel
authors.initials: M
authors.lastname: Blesa
authors.affiliation: MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK.
authors.forename: Emma J
authors.initials: EJ
authors.lastname: Moore
authors.affiliation: MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK.
authors.forename: Rozalia
authors.initials: R
authors.lastname: Pataky
authors.affiliation: MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Sparrow
authors.affiliation: Department of Radiology, Royal Hospital for Sick Children, Edinburgh, UK.
authors.forename: A G
authors.initials: AG
authors.lastname: Wilkinson
authors.affiliation: Clinical Research Imaging Centre, University of Edinburgh, Edinburgh, UK.
authors.forename: Gillian
authors.initials: G
authors.lastname: Macnaught
authors.affiliation: Clinical Research Imaging Centre, University of Edinburgh, Edinburgh, UK.
authors.forename: Scott I
authors.initials: SI
authors.lastname: Semple
authors.affiliation: MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK.|Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
authors.forename: James P
authors.initials: JP
authors.lastname: Boardman
mesh_terms: D001271:Atlases as Topic; D001921:Brain / Q000502:physiology*; D006801:Humans; D007231:Infant, Newborn; D007858:Learning; D008279:Magnetic Resonance Imaging