Documentation/Nightly/Modules/BasicBrainTissues

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

Introduction and Acknowledgements

Extension: BrainTissuesExtension Webpage: http://dcm.ffclrp.usp.br/csim/ 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   CAPES Brazil

Module Description

This module offer a simple and robust brain tissue segmentation focused on white matter, gray matter and CSF brain tissues. The method applied here is based on K-Means clustering segmentation, which presents best results with high quality T1 weighted MRI images.

NOTE: This module can be used alone (only apply the K-Means segmentation method on the input data), but the Brain Structures Segmenter module already use it internally, which control a image processing pipeline for a better brain tissue segmentation result.

Use Cases

• Use Case 1: Separate White Matter, Gray Matter and CSF brain tissues from a strucutral MRI image.
  • There are some image processing strategies that may need a specific brain tissue mask and this module could facilitate this task. For instance, a Multiple Sclerosis lesion detection algorithm may need a White Matter mask in order to define a localized brain region where the lesion are more probable to appear.

• 

  White matter, gray matter and CSF tissues segmented from the previous MRI image

• 

  A white matter mask 3D reconstruction

• 

  A gray matter mask 3D reconstruction

Panels and their use

User Interface

IO:

• Input Volume
  • Input volume. The algorithm works better with high resolution T1 MRI images alread brain extract and inhomogeneity corrected
• Image Modality
  • Select the image modality inserted as a input volume
• Brain Mask
  • Output brain tissue mask

Tissue Type Output:

• Separate one tissue class
  • Choose if you want all the tissues classes or only one class segmented
• Tissue
  • Choose what is the brain tissue label that you want as the output label

Similar Modules

• EM Segmenter

References

N/A