EMSegmenter-Tasks:Non-Human-Primate

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Description

Non Human Primate pipeline ...TODO


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 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: Automatically segment the MRI scan into the structures of interest using EM Algorithm (Pohl et al 2007)

Anatomical Tree

  • Root
    • Head
      • intracranial cavity (ICC)
        • TODO (WGC)
          • grey matter (GM)
            • TODO (lSGM)
              • left caudate (lCaudate)
              • left putamen (lPutamen)
              • left hippocampus (lHippocampus)
            • TODO (rSGM)
              • right caudate (rCaudate)
              • right putamen (rPutamen)
              • right hippocampus (rHippocampus)
            • TODO (CGM)
          • white matter (WM)
          • cerebrospinal fluid (CSF)
        • Brainstem
        • Cerebellum
      • background (BG)

Atlas

Image Dimension = 256 x 256 x 252
Image Spacing = 0.4688 x 0.4688 x 0.50002


EMSegmenter NHP template t1.png EMSegmenter NHP CSF.png EMSegmenter NHP GM.png EMSegmenter NHP WM.png
Template (T1) CSF GM WM

Result

EMSegmenter NHP T1.png
NHP Labelmap.png

Collaborators

Andriy Fedorov (BWH)

Citations