title: Manual-Protocol Inspired Technique for Improving Automated MR Image Segmentation during Label Fusion.
abstract: Recent advances in multi-atlas based algorithms address many of the previous limitations in model-based and probabilistic segmentation methods. However, at the label fusion stage, a majority of algorithms focus primarily on optimizing weight-maps associated with the atlas library based on a theoretical objective function that approximates the segmentation error. In contrast, we propose a novel method-Autocorrecting Walks over Localized Markov Random Fields (AWoL-MRF)-that aims at mimicking the sequential process of manual segmentation, which is the gold-standard for virtually all the segmentation methods. AWoL-MRF begins with a set of candidate labels generated by a multi-atlas segmentation pipeline as an initial label distribution and refines low confidence regions based on a localized Markov random field (L-MRF) model using a novel sequential inference process (walks). We show that AWoL-MRF produces state-of-the-art results with superior accuracy and robustness with a small atlas library compared to existing methods. We validate the proposed approach by performing hippocampal segmentations on three independent datasets: (1) Alzheimer's Disease Neuroimaging Database (ADNI); (2) First Episode Psychosis patient cohort; and (3) A cohort of preterm neonates scanned early in life and at term-equivalent age. We assess the improvement in the performance qualitatively as well as quantitatively by comparing AWoL-MRF with majority vote, STAPLE, and Joint Label Fusion methods. AWoL-MRF reaches a maximum accuracy of 0.881 (dataset 1), 0.897 (dataset 2), and 0.807 (dataset 3) based on Dice similarity coefficient metric, offering significant performance improvements with a smaller atlas library (< 10) over compared methods. We also evaluate the diagnostic utility of AWoL-MRF by analyzing the volume differences per disease category in the ADNI1: Complete Screening dataset. We have made the source code for AWoL-MRF public at: https://github.com/CobraLab/AWoL-MRF.
authors.affiliation: Institute of Biomaterials and Biomedical Engineering, University of TorontoToronto, ON, Canada; Cerebral Imaging Centre, Douglas Mental Health University InstituteVerdun, QC, Canada; Kimel Family Translational Imaging-Genetics Research Lab, Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental HealthToronto, ON, Canada.
authors.forename: Nikhil
authors.initials: N
authors.lastname: Bhagwat
authors.affiliation: Kimel Family Translational Imaging-Genetics Research Lab, Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health Toronto, ON, Canada.
authors.forename: Jon
authors.initials: J
authors.lastname: Pipitone
authors.affiliation: Institute of Biomaterials and Biomedical Engineering, University of TorontoToronto, ON, Canada; Cerebral Imaging Centre, Douglas Mental Health University InstituteVerdun, QC, Canada; Kimel Family Translational Imaging-Genetics Research Lab, Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental HealthToronto, ON, Canada.
authors.forename: Julie L
authors.initials: JL
authors.lastname: Winterburn
authors.affiliation: Neurosciences and Mental Health, The Hospital for Sick Children Research InstituteToronto, ON, Canada; Department of Paediatrics, The Hospital for Sick Children and the University of TorontoToronto, ON, Canada.
authors.forename: Ting
authors.initials: T
authors.lastname: Guo
authors.affiliation: Neurosciences and Mental Health, The Hospital for Sick Children Research InstituteToronto, ON, Canada; Department of Paediatrics, The Hospital for Sick Children and the University of TorontoToronto, ON, Canada.
authors.forename: Emma G
authors.initials: EG
authors.lastname: Duerden
authors.affiliation: Kimel Family Translational Imaging-Genetics Research Lab, Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental HealthToronto, ON, Canada; Department of Psychiatry, University of TorontoToronto, ON, Canada.
authors.forename: Aristotle N
authors.initials: AN
authors.lastname: Voineskos
authors.affiliation: Cerebral Imaging Centre, Douglas Mental Health University InstituteVerdun, QC, Canada; Department of Psychiatry, McGill UniversityMontreal, QC, Canada.
authors.forename: Martin
authors.initials: M
authors.lastname: Lepage
authors.affiliation: Neurosciences and Mental Health, The Hospital for Sick Children Research InstituteToronto, ON, Canada; Department of Paediatrics, The Hospital for Sick Children and the University of TorontoToronto, ON, Canada.
authors.forename: Steven P
authors.initials: SP
authors.lastname: Miller
authors.affiliation: Cerebral Imaging Centre, Douglas Mental Health University InstituteVerdun, QC, Canada; McGill Centre for Studies in AgingMontreal, QC, Canada.
authors.forename: Jens C
authors.initials: JC
authors.lastname: Pruessner
authors.affiliation: Institute of Biomaterials and Biomedical Engineering, University of TorontoToronto, ON, Canada; Cerebral Imaging Centre, Douglas Mental Health University InstituteVerdun, QC, Canada; Department of Psychiatry, McGill UniversityMontreal, QC, Canada; Biological and Biomedical Engineering, McGill UniversityMontreal, QC, Canada.
authors.forename: M Mallar
authors.initials: MM
authors.lastname: Chakravarty
keywords: Alzheimer's disease; MR Imaging; first-episode-psychosis; hippocampus; multi-atlas label fusion; premature birth and neonates; segmentation