Segmentation of neonatal brain MR images using patch-driven level sets

Li Wang, Feng Shi, Gang Li, Yaozong Gao, Weili Lin, John H. Gilmore, Dinggang Shen

Research output: Contribution to journalArticlepeer-review

153 Citations (Scopus)


The segmentation of neonatal brain MR image into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF), is challenging due to the low spatial resolution, severe partial volume effect, high image noise, and dynamic myelination and maturation processes. Atlas-based methods have been widely used for guiding neonatal brain segmentation. Existing brain atlases were generally constructed by equally averaging all the aligned template images from a population. However, such population-based atlases might not be representative of a testing subject in the regions with high inter-subject variability and thus often lead to a low capability in guiding segmentation in those regions. Recently, patch-based sparse representation techniques have been proposed to effectively select the most relevant elements from a large group of candidates, which can be used to generate a subject-specific representation with rich local anatomical details for guiding the segmentation. Accordingly, in this paper, we propose a novel patch-driven level set method for the segmentation of neonatal brain MR images by taking advantage of sparse representation techniques. Specifically, we first build a subject-specific atlas from a library of aligned, manually segmented images by using sparse representation in a patch-based fashion. Then, the spatial consistency in the probability maps from the subject-specific atlas is further enforced by considering the similarities of a patch with its neighboring patches. Finally, the probability maps are integrated into a coupled level set framework for more accurate segmentation. The proposed method has been extensively evaluated on 20 training subjects using leave-one-out cross validation, and also on 132 additional testing subjects. Our method achieved a high accuracy of 0.919. ±. 0.008 for white matter and 0.901. ±. 0.005 for gray matter, respectively, measured by Dice ratio for the overlap between the automated and manual segmentations in the cortical region.

Original languageEnglish
Pages (from-to)141-158
Number of pages18
Publication statusPublished - 2014 Jan 1


  • Atlas based segmentation
  • Coupled level set (CLS)
  • Elastic-net
  • Neonatal brain MRI
  • Sparse representation

ASJC Scopus subject areas

  • Neurology
  • Cognitive Neuroscience


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