title: Brain extraction in pediatric ADC maps, toward characterizing neuro-development in multi-platform and multi-institution clinical images.
abstract: Apparent Diffusion Coefficient (ADC) maps can be used to characterize myelination and to detect abnormalities in the developing brain. However, given the normal variation in regional ADC with myelination, detection of abnormalities is difficult when based on visual assessment. Quantitative and automated analysis of pediatric ADC maps is thus desired but requires accurate brain extraction as the first step. Currently, most existing brain extraction methods are optimized for structural T1-weighted MR images of fully myelinated brains. Due to differences in age and image contrast, these approaches do not translate well to pediatric ADC maps. To address this problem, we present a multi-atlas brain extraction framework that has 1) specificity: designed and optimized specifically for pediatric ADC maps; 2) generality: applicable to multi-platform and multi-institution data, and to subjects at various neuro-developmental stages across the first 6 years of life; 3) accuracy: highly accurate compared to expert annotations; and 4) consistency: consistently accurate regardless of sources of data and ages of subjects. We show how we achieve these goals, via optimizing major components in a multi-atlas brain extraction framework, and via developing and evaluating new criteria for its atlas ranking component. Moreover, we demonstrate that these goals can be achieved with a fixed set of atlases and a fixed set of parameters, which opens doors for our optimized framework to be used in large-scale and multi-institution neuro-developmental and clinical studies. In a pilot study, we use this framework in a dataset containing scanner-generated ADC maps from 308 pediatric patients collected during the course of routine clinical care. Our framework leads to successful quantifications of the changes in whole-brain volumes and mean ADC values across the first 6 years of life.
authors.affiliation: Psychiatric Neuroimaging, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 120 2nd Ave, Charlestown, MA 02129, USA; Laboratory for Computational Neuroimaging, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, 149 13th St, Charlestown, MA 02129, USA. Electronic address: yangming.ou@mgh.harvard.edu.
authors.forename: Yangming
authors.initials: Y
authors.lastname: Ou
authors.affiliation: Psychiatric Neuroimaging, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 120 2nd Ave, Charlestown, MA 02129, USA; Laboratory for Computational Neuroimaging, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, 149 13th St, Charlestown, MA 02129, USA.
authors.forename: Randy L
authors.initials: RL
authors.lastname: Gollub
authors.affiliation: Psychiatric Neuroimaging, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 120 2nd Ave, Charlestown, MA 02129, USA; Laboratory for Computational Neuroimaging, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, 149 13th St, Charlestown, MA 02129, USA.
authors.forename: Kallirroi
authors.initials: K
authors.lastname: Retzepi
authors.affiliation: Psychiatric Neuroimaging, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 120 2nd Ave, Charlestown, MA 02129, USA; Laboratory for Computational Neuroimaging, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, 149 13th St, Charlestown, MA 02129, USA.
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Reynolds
authors.affiliation: Fetal-Neonatal Neuroimaging and Developmental Science Center, Children's Hospital Boston, Harvard Medical School, 1 Autumn St, Boston, MA 02115, USA.
authors.forename: Rudolph
authors.initials: R
authors.lastname: Pienaar
authors.affiliation: Isomics, Inc., 55 Kirkland St, Cambridge, MA 02138, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Pieper
authors.affiliation: Research Computing, Partners HealthCare, 1 Constitution Center, Charlestown, MA 02129, USA; Laboratory of Computer Science, Massachusetts General Hospital, Harvard Medical School, 50 Staniford St, Boston, MA 02114, USA.
authors.forename: Shawn N
authors.initials: SN
authors.lastname: Murphy
authors.affiliation: Fetal-Neonatal Neuroimaging and Developmental Science Center, Children's Hospital Boston, Harvard Medical School, 1 Autumn St, Boston, MA 02115, USA.
authors.forename: P Ellen
authors.initials: PE
authors.lastname: Grant
authors.affiliation: Laboratory for Computational Neuroimaging, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, 149 13th St, Charlestown, MA 02129, USA.
authors.forename: Lilla
authors.initials: L
authors.lastname: Zöllei
mesh_terms: D000465:Algorithms; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology* / Q000254:growth & development*; D002648:Child; D002675:Child, Preschool; D038524:Diffusion Magnetic Resonance Imaging / Q000379:methods*; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D009186:Myelin Sheath / Q000502:physiology*; D015203:Reproducibility of Results; D012815:Signal Processing, Computer-Assisted