EMSegmenter-Tasks:Template

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Description

-- Data Assumption
-- description of pipeline with citations to algorithms used

Anatomical Tree

-- Define Anatomical Tree used in mrml file - first list the complete name and then the abbreviating used in the mrml file

• root
  • background (BG)
    • air (AIR)

Atlas

- how did you construct the atlas ?
-- what did you do for skull stripping or any other preprocessing
-- What did you do for group registration
-- how did you generate the segmentations
-- how many set of images did you use
-- where did you get the data from
-- example images of atlas

Atlas was generated based on 82 scans and corresponding segmentations provided by Psychiatry Neuroimaging Laboratory, BWH. We registered the scans to a preselected template via Warfield et al. 2001.
Image Dimension = 256 x 256 x 124
Image Spacing = 0.9375 x 0.9375 x 1.5

Template (T1)	CSF	GM	WM

Result

Acknowledgment

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

Citations

• 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.