Combining multi-atlas segmentation with brain surface estimation

Yuankai Huo, Aaron Carass, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince, Bennett A. Landman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitation in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2016
Subtitle of host publicationImage Processing
EditorsMartin A. Styner, Elsa D. Angelini, Elsa D. Angelini
PublisherSPIE
ISBN (Electronic)9781510600195
DOIs
StatePublished - 2016
EventMedical Imaging 2016: Image Processing - San Diego, United States
Duration: Mar 1 2016Mar 3 2016

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
Volume9784
ISSN (Print)1605-7422

Other

OtherMedical Imaging 2016: Image Processing
CountryUnited States
CitySan Diego
Period3/1/163/3/16

Keywords

  • Cerebral Cortex
  • Cortical Reconstruction
  • Magnetic Resonance Imaging
  • Multi-atlas Segmentation

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging

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