EMSegmenter-Tasks:MRI-Human-Brain-Parcellation

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Description

MRI Human Head pipeline for a finer-grained parcellation (TODO: Priya please provide description and proper citation)

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

The anatomical tree represents the structures to be segmented. Node labels displayed below contain a human readable structure name and in parentheses the internally used structure name.

  • Root
    • background (BG)
    • grey matter (GM)
      • left temporal grey matter (LTGM)
        • left temporal grey matter - region 1 (LTGM1)
        • left temporal grey matter - region 2 (LTGM2)
        • left temporal grey matter - region 3 (LTGM3)
        • left temporal grey matter - region 4 (LTGM4)
      • right temporal grey matter (RTGM)
        • right temporal grey matter - region 1 (RTGM1)
        • right temporal grey matter - region 2 (RTGM2)
        • right temporal grey matter - region 3 (RTGM3)
        • right temporal grey matter - region 4 (RTGM4)
      • subcortical grey matter (SUBGM)
    • white matter (WM)
      • left temporal white matter (LTWM)
        • left temporal white matter - region 1 (LTWM1)
        • left temporal white matter - region 2 (LTWM2)
        • left temporal white matter - region 3 (LTWM3)
        • left temporal white matter - region 4 (LTWM4)
      • right temporal white matter (RTWM)
        • right temporal white matter - region 1 (RTWM1)
        • right temporal white matter - region 2 (RTWM2)
        • right temporal white matter - region 3 (RTWM3)
        • right temporal white matter - region 4 (RTWM4)
      • subcortical white matter (SUBWM)
    • cerebrospinal fluid (CSF)

Atlas

The atlas hes been created by Padmapriya Srinivasan and Sylvain Bouix from (PNL-BWH)

Image Dimension = 256 x 256 x 220
Image Spacing = 0.9375 x 0.9375 x 0.9375

TODO, some details about the combined atlas


EMSegmenter MRIHumanBrainParcellation t1.png EMSegmenter MRIHumanBrainParcellation csf.png EMSegmenter MRIHumanBrainParcellation ltgm1.png EMSegmenter MRIHumanBrainParcellation ltwm1.png
Template (T1) CSF Left Temporal GM Left Temporal WM


Result

MRI-Human-Brain-Parcellation T1 3x360x360.png MRI-Human-Brain-Parcellation 3x360x360.png

Collaborators

Padmapriya Srinivasan and Sylvain Bouix (PNL-BWH)

Acknowledgment

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

Citations