EMSegmenter-Tasks:Template

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Home < EMSegmenter-Tasks:Template

Return to EMSegmenter Task Overview Page

This wiki template can be used for new tasks

Description

Single channel automatic segmentation of t1w-MRI brain scans into the major tissue classes (gray matter, white matter, csf). The task can only be applied to t1w brain scan showing parts of the skull and neck. The pipeline consist of the following steps:

Anatomical Tree

  • root
    • background (BG)
      • air (AIR)
    • intracranial cavity (ICC)
      • white matter (WM)

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

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

EMSegmenter MRI-Human-Brain Template 420x420.png EMSegmenter MRI-Human-Brain CSF 420x420.png EMSegmenter MRI-Human-Brain GM 420x420.png EMSegmenter MRI-Human-Brain WM 420x420.png
Template (T1) CSF GM WM

Result

MRI-Human-Brain-T1.png
MRI-Human-Brain-Labelmap.png

Acknowledgment

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

Citations