Subject specific sparse dictionary learning for atlas based brain mri segmentation

Snehashis Roy, Aaron Carass, Jerry L. Prince, Dzung L. Pham

Research output: Contribution to journalArticlepeer-review


Quantitative measurements from segmentations of soft tissues from magnetic resonance images (MRI) of human brains provide important biomarkers for normal aging, as well as disease progression. In this paper, we propose a patch-based tissue classification method from MR images using sparse dictionary learning from an atlas. Unlike most atlas-based classification methods, deformable registration from the atlas to the subject is not required. An “atlas” consists of an MR image, its tissue probabilities, and the hard segmentation. The “subject” consists of the MR image and the corresponding affine registered atlas probabilities (or priors). A subject specific patch dictionary is created by learning relevant patches from the atlas. Then the subject patches are modeled as sparse combinations of learned atlas patches. The same sparse combination is applied to the segmentation patches of the atlas to generate tissue memberships of the subject. The novel combination of prior probabilities in the example patches enables us to distinguish tissues having similar intensities but having different spatial location. We show that our method outperforms two state-of-the-art whole brain tissue segmentation methods. We experimented on 12 subjects having manual tissue delineations, obtaining mean Dice coefficients of 0.91 and 0.87 for cortical gray matter and cerebral white matter, respectively. In addition, experiments on subjects with ventriculomegaly shows significantly better segmentation using our approach than the competing methods.


  • Hallucination
  • Image synthesis
  • Intensity normalization
  • Patches

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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