Automated segmentation of three-dimensional MR brain images

Jonggeun Park, Byungjun Baek, Choong Il Ahn, Kyo Bum Ku, Dong Kyun Jeong, Chulhee Lee

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

1 Citation (Scopus)


Brain segmentation is a challenging problem due to the complexity of the brain. In this paper, we propose an automated brain segmentation method for 3D magnetic resonance (MR) brain images which are represented as a sequence of 2D brain images. The proposed method consists of three steps: pre-processing, removal of non-brain regions (e.g., the skull, meninges, other organs, etc), and spinal cord restoration. In pre-processing, we perform adaptive thresholding which takes into account variable intensities of MR brain images corresponding to various image acquisition conditions. In segmentation process, we iteratively apply 2D morphological operations and masking for the sequences of 2D sagittal, coronal, and axial planes in order to remove non-brain tissues. Next, final 3D brain regions are obtained by applying OR operation for segmentation results of three planes. Finally we reconstruct the spinal cord truncated during the previous processes. Experiments are performed with fifteen 3D MR brain image sets with 8-bit gray-scale. Experiment results show the proposed algorithm is fast, and provides robust and satisfactory results.

Original languageEnglish
Title of host publicationMedical Imaging 2006
Subtitle of host publicationImage Processing
Publication statusPublished - 2006
EventMedical Imaging 2006: Image Processing - San Diego, CA, United States
Duration: 2006 Feb 132006 Feb 16

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
Volume6144 III
ISSN (Print)1605-7422


OtherMedical Imaging 2006: Image Processing
Country/TerritoryUnited States
CitySan Diego, CA

All Science Journal Classification (ASJC) codes

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


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