Difference between revisions of "EMSegmenter-Tasks:Non-Human-Primate"
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=Description= | =Description= | ||
Non Human Primate pipeline ...'''TODO''' | Non Human Primate pipeline ...'''TODO''' | ||
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| + | The pipeline consist of the following steps: | ||
| + | * Step 1: Perform image inhomogeneity correction of the MRI scan via [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection] (Tustison et al 2010) | ||
| + | * Step 2: Register the atlas to the MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007) | ||
| + | * Step 3: Compute the intensity distributions for each structure <BR> | ||
| + | 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 [[Modules:EMSegmenter-3.6|EM Algorithm]] (Pohl et al 2007) | ||
=Anatomical Tree= | =Anatomical Tree= | ||
Revision as of 23:25, 1 December 2010
Home < EMSegmenter-Tasks:Non-Human-PrimateReturn to EMSegmenter Task Overview Page
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)
- TODO (lSGM)
- white matter (WM)
- cerebrospinal fluid (CSF)
- grey matter (GM)
- Brainstem
- Cerebellum
- TODO (WGC)
- background (BG)
- intracranial cavity (ICC)
- Head
Atlas
Image Dimension = 256 x 256 x 252
Image Spacing = 0.4688 x 0.4688 x 0.50002
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| Template (T1) | CSF | GM | WM |
Result
Collaborators
Andriy Fedorov (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
