Integration of sparse multi-modality representation and anatomical constraint for isointense infant brain MR image segmentation

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

Research output: Contribution to journalArticlepeer-review

91 Citations (Scopus)


Segmentation of infant brain MR images is challenging due to poor spatial resolution, severe partial volume effect, and the ongoing maturation and myelination processes. During the first year of life, the brain image contrast between white and gray matters undergoes dramatic changes. In particular, the image contrast inverses around 6-8. months of age, where the white and gray matter tissues are isointense in T1 and T2 weighted images and hence exhibit the extremely low tissue contrast, posing significant challenges for automated segmentation. In this paper, we propose a general framework that adopts sparse representation to fuse the multi-modality image information and further incorporate the anatomical constraints for brain tissue segmentation. Specifically, we first derive an initial segmentation from a library of aligned images with ground-truth segmentations by using sparse representation in a patch-based fashion for the multi-modality T1, T2 and FA images. The segmentation result is further iteratively refined by integration of the anatomical constraint. The proposed method was evaluated on 22 infant brain MR images acquired at around 6. months of age by using a leave-one-out cross-validation, as well as other 10 unseen testing subjects. Our method achieved a high accuracy for the Dice ratios that measure the volume overlap between automated and manual segmentations, i.e., 0.889 ± 0.008 for white matter and 0.870 ± 0.006 for gray matter.

Original languageEnglish
Pages (from-to)152-164
Number of pages13
Publication statusPublished - 2014 Apr 1

Bibliographical note

Funding Information:
The authors would like to thank the editor and anonymous reviewers for their constructive comments and suggestions. This work was supported in part by the National Institutes of Health grants EB006733 , EB008374 , EB009634 , AG041721 , MH100217 , and AG042599 . This work was also partially supported by the National Research Foundation grant (No. 2012-005741 ) funded by the Korean government.


  • Anatomical constraint
  • Infant brain images
  • Isointense stage
  • Low contrast
  • Sparse representation
  • Tissue segmentation

ASJC Scopus subject areas

  • Neurology
  • Cognitive Neuroscience


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