EMSegmenter-Tasks

Return to EMSegmenter Overview Page

What is a task?

Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on the used input data. The signal level in the input data varies with the used image modalities (e.g. MRI, CT, ...) and with each anatomical structure. The EMSegmenter can take advantage of some knowledge about the signal level of those anatomical structures in the different image modalities.
Technically, each tasks consist of a .mrml file and a .tcl file.
The .mrml file stores the anatomical properties (mean values, covariance values) in a user defined tree structure.
The .tcl script is used to perform some pre-processing on the input data.

Visit the following web page to create your own task.

Segmentation Task Library

Existing Tasks in Slicer 3.6.3

• Task 01: MRI Human Brain for non-skull stripped T1 scans
• Task 02: MRI Human Brain Parcellation for skull stripped T1 scans
• Task 03: Non-Human Primate for skull stripped T1 scans

Tasks in development for Slicer 3.6.4

• Task 04: CT Hand Bone
• Task 05: MRI Human Brain Full Parcellation for non-skull stripped T1 scans
• Task 06: MRI Human Brain with high in-plane resolution for non-skull stripped T1 scans
• Task 07: MRI Human Brain Experimental with skull stripping
• Task 08: Human Eye

EMSegmenter use cases

Quantitative assessment using MPRAGE and Flair images

• Collaborator: Tammie Benzinger , Washington University School of Medicine
• Short description: Quantitative assessment using MPRAGE and Flair images
• Image specification: Dimension: 256x256x160 , Spacing 1x1x1, T2 MPRAGE
• Used Task: MRI Human Brain Experimental (with skull stripping)

Aging Study

• Collaborator: Alexander Zaitsev, Brigham and Women's Hospital
• Short description:
• Image specification:
• Used Task: MRI Human Brain

• 
• 

HIV Study

• Collaborator: Alexander Zaitsev, Brigham and Women's Hospital
• Short description:
• Image specification:
• Used Task: MRI Human Brain

• 
• 

MS Study

• Collaborator: Alexander Zaitsev, Brigham and Women's Hospital
• Short description:
• Image specification:
• Used Task: MRI Human Brain

• 

Social Cognition Study

• Collaborator: Alexander Zaitsev, Brigham and Women's Hospital, Pecs University
• Short description: Evaluate brain atrophy for elderly MS patients.
• Image specification: 3 Tesla Scanner: Magnetom TIM Trio, Siemens, 3D MPRAGE, Slice thickness: 1.2mm, Spacing 1.2 1 1 (mm)
• Used Task: MRI Human Brain

•