Fast method for brain image segmentation: Application to proton magnetic resonance spectroscopic imaging

David Bonekamp, Alena Horská, Michael A. Jacobs, Atilla Arslanoglu, Peter B. Barker

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


The interpretation of brain metabolite concentrations measured by quantitative proton magnetic resonance spectroscopic imaging (MRSI) is assisted by knowledge of the percentage of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) within each MRSI voxel. Usually, this information is determined from T1-weighted magnetic resonance images (MRI) that have a much higher spatial resolution than the MRSI data. While this approach works well, it is time-consuming. In this article, a rapid data acquisition and analysis procedure for image segmentation is described, which is based on collection of several, thick slice, fast spin echo images (FSE) of different contrast. Tissue segmentation is performed with linear "Eigenimage" filtering and normalization. The method was compared to standard segmentation techniques using high-resolution 3D T1-weighted MRI in five subjects. Excellent correlation between the two techniques was obtained, with voxel-wise regression analysis giving GM: R2 = 0.893 ± 0.098, WM: R 2 = 0.892 ± 0.089, In(CSF): R2 = 0.831 ± 0.082). Test-retest analysis in one individual yielded an excellent agreement of measurements with R2 higher than 0.926 in all three tissue classes. Application of FSE/EI segmentation to a sample proton MRSI dataset yielded results similar to prior publications. It is concluded that FSE imaging in conjunction with Eigenimage analysis is a rapid and reliable way of segmenting brain tissue for application to proton MRSI.

Original languageEnglish (US)
Pages (from-to)1268-1272
Number of pages5
JournalMagnetic resonance in medicine
Issue number5
StatePublished - Nov 2005


  • Brain
  • Eigenimage filter
  • Magnetic resonance spectroscopic imaging
  • Partial volume correction
  • Tissue class segmentation

ASJC Scopus subject areas

  • Radiology Nuclear Medicine and imaging


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