Documentation/4.1/Modules/BRAINSMush
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BRAINSMush
BRAINSMush
General Information
Module Type & Category
Type: CLI
Category: Segmentation
Authors, Collaborators & Contact
- Ronald Pierson, University of Iowa
- Gregory Harris, University of Iowa
- Hans Johnson, PhD: University of Iowa
- Steven A. Dunn: University of Iowa
- Vincent Magnotta, PhD: University of Iowa
- Contact: Vincent Magnotta, vincent-magnotta@uiowa.edu
Module Description
BRAINSMush uses the Maximize Uniformity Summation Heuristic(MUSH), as developed at the University of Iowa, to extract the brain and surface CSF from a multi-modal imaging study. It forms a linear combination of multi-modal MR imaging data to make the signal intensity within the brain as uniform as possible. This resulting image is then thresholded to obtain the brain and surface CSF region.
This method was applied to a sample of 20 MR brain scans and its results were compared to those obtained by 3dSkullStrip, 3dIntracranial, BET and BET2. The average Jaccard metrics for the twenty subjects was 0.66(BET), 0.61(BET2), 0.88(3dIntracranial), 0.91(3dSkullStrip) and 0.94(MUSH).
Usage
Use Cases, Examples
This module is especially appropriate for these use cases:
- Use Case 1:
- Use Case 2:
Examples of the module in use:
- Example 1
- Example 2
Tutorials
Links to tutorials explaining how to use this module:
- Tutorial 1
- Data Set 1
Quick Tour of Features and Use
A list panels in the interface, their features, what they mean, and how to use them. For instance:
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Development
Notes from the Developer(s)
Algorithms used, library classes depended upon, use cases, etc.
Dependencies
Other modules or packages that are required for this module's use.
Tests
On the Dashboard, these tests verify that the module is working on various platforms:
- MyModuleTest1 MyModuleTest1.cxx
- MyModuleTest2 MyModuleTest2.cxx
Known bugs
Links to known bugs in the Slicer3 bug tracker
Usability issues
Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.
Source code & documentation
Links to the module's source code:
Source code:
Doxygen documentation:
More Information
Acknowledgment
Include funding and other support here.
References
Publications related to this module go here. Links to pdfs would be useful.
