Difference between revisions of "Documentation/Nightly/Extensions/BrainTissuesExtension"

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{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
Most frequently used for these scenarios:
 
Most frequently used for these scenarios:
* Use Case 1: a
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* Use Case 1: Specific tissue classification and study
**b
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** There are several quantitative approaches that are applied only in a certain tissue type (for instance, cortical thickness) in which a previous brain segmentation could be needed.
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* Use Case 2: Restrict areas for image quantitative analysis
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** A white matter could be used for specific measurements in some diseases, for example, in Multiple Sclerosis it could be useful to define only the white matter region in order to test a automatic segmentation algorithm.
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<gallery widths="200px" perrow="3">
 
<gallery widths="200px" perrow="3">
Image:MRI_raw.png|Raw T1 weighted MRI Image
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Image:T1_fullBrain.png|A T1 weighted MRI image illustrating a usual brain
Image:MRI_AAD.png|T1 weighted MRI Image with AAD filter (q=1.2)
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Image:T1_tissues.png|White matter, gray matter and CSF tissues segmented from the previous MRI image
Image:MRI_IAD.png|T1 weighted MRI Image with IAD filter (q=1.2)
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Image:WM_3DReconstruction.png|A 3D reconstruction using only the white matter mask
Image:DTI_FA_raw.png|DTI-FA map without image filtering process
 
Image:DTI_FA_AAD.png|DTI-FA map with AAD image filtering (q=0.4)
 
 
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{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
 
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
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[https://www.slicer.org/wiki/Modules:EMSegmenter-3.6 EM Segmenter]
  
 
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Revision as of 00:54, 26 November 2016

Home < Documentation < Nightly < Extensions < BrainTissuesExtension


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

This work was partially funded by CAPES and CNPq, a Brazillian Agencies. Information on CAPES can be obtained on the CAPES website and CNPq website.
Author: Antonio Carlos da S. Senra Filho, CSIM Laboratory (University of Sao Paulo, Department of Computing and Mathematics)
Contact: Antonio Carlos da S. Senra Filho <email>acsenrafilho@usp.br</email>

CSIM Laboratory  
University of Sao Paulo  
CNPq Brazil  
CAPES Brazil  


Extension Description

BrainTissuesExtension-logo.png

Brain tissue segmentation plays an important role in many different image processing steps, which can offer a possibility to study different parts of the brain in different hypothesis, such as neurodegenerative disease progression and global brain structural quantitative parameters (brain atrophy, for instance). For this reason, tissue segmentation procedures have been intensively studied in the recent years. This extension aims to offer a fast, reliable and simple solutions for brain tissue segmentation, in which are separated in different modules. See the modules list below to find the most appropriate tool for your study.

Modules

Use Cases

Most frequently used for these scenarios:

  • Use Case 1: Specific tissue classification and study
    • There are several quantitative approaches that are applied only in a certain tissue type (for instance, cortical thickness) in which a previous brain segmentation could be needed.
  • Use Case 2: Restrict areas for image quantitative analysis
    • A white matter could be used for specific measurements in some diseases, for example, in Multiple Sclerosis it could be useful to define only the white matter region in order to test a automatic segmentation algorithm.

Similar Extensions

EM Segmenter

References

  • paper

Information for Developers


Repositories: