Difference between revisions of "EMSegmenter-Tasks:LesionExp"

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Image:EMS LesionExp T1.png
Image:EMS LesionExp FLAIR.png
Image:EMS LesionExp Segmentation.png

Revision as of 23:20, 18 June 2011

Home < EMSegmenter-Tasks:LesionExp

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Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gray matter, white matter, csf). The pipeline consist of the following steps:

  • Step 1: Perform image inhomogeneity correction of the MRI scan via N4ITKBiasFieldCorrection (Tustison et al 2010)
  • Step 2: Register the atlas to the T1 MRI scan via BRAINSFit (Johnson et al 2007)
  • Step 3: Compute the intensity distributions for each structure

Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas.

  • Step 4: Assign T1 GM intensity distribution to T1 Lesion intensity distribution
  • Step 5: Automatically segment the MRI scan into the structures of interest using EM Algorithm (Pohl et al 2007)

Anatomical Tree

  • root
    • background (BG)
    • intracranial cavity (ICC)
      • white matter (WM)
      • grey matter (GM)
      • cerebrospinal fluid (CSF)
      • Lesion


Atlas was generated based on 82 scans and corresponding segmentations provided by Psychiatry Neuroimaging Laboratory, BWH. We registered the scans to a preselected template via Warfield et al. 2001.
Image Dimension = 256 x 256 x 124
Image Spacing = 0.9375 x 0.9375 x 1.5

EMSegmenter MRI-Human-Brain Template 420x420.png EMSegmenter MRI-Human-Brain CSF 420x420.png EMSegmenter MRI-Human-Brain GM 420x420.png EMSegmenter MRI-Human-Brain WM 420x420.png
Template (T1) CSF GM WM



The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.