EMSegmenter-Tasks:MRI-Human-Brain-Parcellation

Description

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

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 atlas

Pre-Processing

• 1 step: image inhomogeneity correction N4ITKBiasFieldCorrection
• 2 step: atlas-to-target registration BRAINSFit
• 3 step: automatic mean/covariance calculation. (TODO Kilian)

Result

Collaborators

Padmapriya Srinivasan and Sylvain Bouix (PNL-BWH)

Citations

• Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC N4ITK: Improved N3 Bias Correction, IEEE Trans Med Imag, 2010
• Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. A Hierarchical Algorithm for MR Brain Image Parcellation. IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
• S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.
• Johnson H.J., Harris G., Williams K. BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, The Insight Journal, July 2007