Difference between revisions of "EMSegmenter-Tasks:MRI-Human-Brain-Parcellation"

From Slicer Wiki
Jump to: navigation, search
Line 19: Line 19:
 
**** right temporal grey matter - region 3 (RTGM3)
 
**** right temporal grey matter - region 3 (RTGM3)
 
**** right temporal grey matter - region 4 (RTGM4)
 
**** right temporal grey matter - region 4 (RTGM4)
*** '''TODO''' (SUBGM)
+
*** subcortical grey matter (SUBGM)
 
** white matter (WM)
 
** white matter (WM)
 
*** left temporal white matter (LTWM)
 
*** left temporal white matter (LTWM)
Line 31: Line 31:
 
**** right temporal white matter - region 3 (RTWM3)
 
**** right temporal white matter - region 3 (RTWM3)
 
**** right temporal white matter - region 4 (RTWM4)
 
**** right temporal white matter - region 4 (RTWM4)
*** '''TODO''' (SUBWM)
+
*** subcortical white matter (SUBWM)
 
** cerebrospinal fluid (CSF)
 
** cerebrospinal fluid (CSF)
  

Revision as of 18:05, 30 November 2010

Home < 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

MRIHumanBrainParcellation.png

TODO: New Screenshots (Dominique)

  • T1(3 views)
  • Labelmap(3 views)

Collaborators

Padmapriya Srinivasan and Sylvain Bouix (PNL-BWH)