2011 Summer Project Week Customizing EMSegmenter pipelines for brain lesions
Customizing EMSegmenter pipelines for brain lesions
Key Investigators
- University of Pennsylvania: Dominique Belhachemi
- University of Pennsylvania: Kilian Pohl
- Brigham and Women's Hospital: Alex Zaitsev
Objective
The goal is to segment white matter lesions based on T1 and FLAIR brain scans.
Approach, Plan
We want to use the EMSegmenter module for this project. The plan is to create a two channel pipeline which includes pre-processing (e.g. registration) and applying the EM algorithm to perform the segmentation.
Progress
We created a 2 channnel(T1+FLAIR) pipeline for this project. Intensity values of the lesions are calculated automatic but have to manually updated to get a better result. (see segmentation screenshot)
Open: With this approach we detect a lot of false positives outside the white matter region.
References
Segmentation result
FLAIR scan
T1 scan
https://www.slicer.org/wiki/EMSegmenter-Tasks
Delivery Mechanism
This work will be delivered to the NAMIC Kit as part of the EMSegmenter module.
