Optimization of tissue segmentation of brain MR images based on multispectral 3D feature maps

Feroze B. Mohamed, Simon Vinitski, Scott H. Faro, Carlos F. Gonzalez, John Mack, Tad Iwanaga

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


The purpose of this work was to optimize and increase the accuracy of tissue segmentation of the brain magnetic resonance (MR) images based on multispectral 3D feature maps. We used three sets of MR images as input to the in-house developed semi-automated 3D tissue segmentation algorithm: proton density (PD) and T2-weighted fast spin echo and, T1-weighted spin echo. First, to eliminate the random noise, non-linear anisotropic diffusion type filtering was applied to all the images. Second, to reduce the nonuniformity of the images, we devised and applied a correction algorithm based on uniform phantoms. Following these steps, the qualified observer 'seeded' (identified training points) the tissue of interest. To reduce the operator dependent errors, cluster optimization was also used; this clustering algorithm identifies the densest clusters pertaining to the tissues. Finally, the images were segmented using k-NN (k-Nearest Neighborhood) algorithm and a stack of color-coded segmented images were created along with the connectivity algorithm to generate the entire surface of the brain. The application of pre-processing optimization steps substantially improved the 3D tissue segmentation methodology.

Original languageEnglish (US)
Pages (from-to)403-409
Number of pages7
JournalMagnetic Resonance Imaging
Issue number3
StatePublished - Apr 1999


  • Image nonuniformity
  • Tissue segmentation

ASJC Scopus subject areas

  • Biophysics
  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging


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