Documentation/4.10/Modules/BabyBrainSegmentation

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Introduction and Acknowledgements

Extension: Baby Brain 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 application to the Anisotropic Anomalous Diffusion (AAD) filter, which is able to increase the image SNR and preserve fine object's details around the image space. This method was studied on MRI structural images (T1 and T2), which other imaging modalities could be properly investigated in the future.

Use Cases

• Use Case 1: ...
  • When dealing with

• 

  Raw T1 weighted MRI Image

• 

  T1 weighted MRI Image with AAD filter (q=1.2)

Panels and their use

User Interface

IO:

• Input Volume
  • Select the input image
• Output Volume
  • Set the output image file which the filters should place the final result

Diffusion Parameters:

• Conductance
  • The conductance regulates the diffusion intensity in the neighborhood area. Choose a higher conductance if the input image has strong noise seem in the whole image space.
• Use Auto Conductance
  • Choose if you want to use an automatic adjustment of conductance parameter. If this is checked, the inserted value is ignored and the optimization function below is used.
• Optimization Function
  • A set of optimization function for automatic estimation of conductance parameter. This is helpful is you do not have an initial guess on what value is appropriate to the conductance setting. (Canny, MAD and Morphological). Please see the Insight-Journal article that explain each of these automatic conductance adjustment methods.
• Number of Iteractions
  • The number of iterations regulates the numerical simulation of the anomalous process over the image. This parameters is also related with the de-noising intensity, however it is more sensible to the noise intensity. Choose the higher number of iterations if the image presents high intensity noise which is not well treated by the conductance parameter.
• Time Step
  • The time step is a normalization parameters for the numerical simulation. The maximum value, given as default, is set to 3D images. Lower time step restrict the numerical simulation of the anomalous process.
• Anomalous parameter
  • The anomalous parameter (or q value) is the generalization parameters responsible to give the anomalous process approach on the diffusion equation. See the reference paper to choose the appropriate q value (at moment, only tested in MRI T1 and T2 weighted images).

Similar Modules

• IAD Image Filter
• Gradient Anisotropic Image Filter

References

• Senra Filho, A.C. & Murta Junior, L. O., 2017. Automatic Conductance Estimation Methods for Anisotropic Diffusion ITK Filters. Insight-Journal. website: http://www.insight-journal.org/browse/publication/983
• da S Senra Filho, A.C., Garrido Salmon, C.E. & Murta Junior, L.O., 2015. Anomalous diffusion process applied to magnetic resonance image enhancement. Physics in Medicine and Biology, 60(6), pp.2355–2373. DOI: 10.1088/0031-9155/60/6/2355
• Filho, A.C. da S.S. et al., 2014. Anisotropic Anomalous Diffusion Filtering Applied to Relaxation Time Estimation in Magnetic Resonance Imaging. In Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, pp. 3893–3896.
• Filho, A.C. da S.S., Barizon, G.C. & Junior, L.O.M., 2014. Myocardium Segmentation Improvement with Anisotropic Anomalous Diffusion Filter Applied to Cardiac Magnetic Resonance Imaging. In Annual Meeting of Computing in Cardiology.