Automatic segmentation of MR brain images in multiple sclerosis patients

Ramesh T.V. Avula, Bradley J. Erickson

Research output: Contribution to journalConference articlepeer-review


A totally automatic scheme for segmenting brain from extracranial tissues and to classify all intracranial voxels as CSF, gray matter(GM), white matter(WM) or abnormality such as multiple sclerosis (MS) lesions is presented in this paper. It is observed that in MR head images, if a tissue's intensity values are normalized, its relationship to the other tissues is essentially constant for a given type of image. Based on this approach, the subcutaneous fat surrounding the head is normalized to classify other tissues. Spatially registered 3 mm MR head image slices of T1 weighted, fast spin echo (dual echo T2 weighted and proton density(PD) weighted images) and fast Fluid Attenuated Inversion Recovery(FLAIR) sequences are used for segmentation. Subcutaneous fat surrounding the skull was identified based on intensity thresholding from T1 weighted images. A multiparametric space map was developed for CSF, GM and WM by normalizing each tissue with respect to the mean value of corresponding subcutaneous fat on each pulse sequence. To reduce the low frequency noise without blurring the fine morphological high frequency details, an anisotropic diffusion filter was applied to all images before segmentation. An initial slice by slice classification was followed by morphological operations to delete any bridges connecting extracranial segments. Finally 3-dimensional region growing of the segmented brain extracts GM, WM and pathology. The algorithm was tested on sequential scans of 10 patients with MS lesions. For well registered sequences, tissues and pathology have been accurately classified. This procedure does not require user input or image training data sets, and shows promise for automatic classification of brain and pathology.

Original languageEnglish (US)
Pages (from-to)960-966
Number of pages7
JournalProceedings of SPIE - The International Society for Optical Engineering
StatePublished - 1996
EventMedical Imaging 1996 Image Processing - Newport Beach, CA, United States
Duration: Feb 12 1996Feb 15 1996


  • Anisotropic diffusion filter
  • Automatic Multiparametric Classification
  • Brain
  • FLAIR sequence
  • Multiple sclerosis lesions
  • Spatially registered MR images
  • Subcutaneous fat tissue

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering


Dive into the research topics of 'Automatic segmentation of MR brain images in multiple sclerosis patients'. Together they form a unique fingerprint.

Cite this