Documentation/Nightly/Extensions/AnomalousFilters

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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

Anomalous diffusion processes (ADP) are mathematically denoted by a power law in the Fokker-Planck equation, leading to the generalized form. There are several generalizations of the Fokker-Plank equation, which should give many different partial differential equations (PDEs). Here we adopted the so-called porous media equation, allowing the super-diffusive and the sub-diffusive processes . In porous media, channels are created promoting or blocking the flow of the density function, which has been proved to provide a suitable application for MRI noise attenuation .

Basically, there are two different filters already implementing the anomalous diffusion process: the isotropic anomalous diffusion and anisotropic anomalous diffusion filters . These filters were already applied on different imaging MR modalities, such as structural T1 and T2 images , diffusion-weighted images (DWI and DTI), MRI relaxation T1 and T2 relaxometry and to fMRI as an initial study.

Modules

• Structural image denoising with tissues border preservation function: AAD Image Filter
• Structural image denoising without tissues border preservation function: IAD Image Filter
• Diffusion-weighted MR image denoising with tissues border preservation: AAD on DWI Image
• Echo-planar imaging denoising with tissues border preservation (fMRI and ASL): AAD on EPI Image

Use Cases

Most frequently used for these scenarios:

• Use Case 1: Noise reduction as a pre-processing step for tissue segmentation
  • When dealing with single voxel classification schemes, a noise reduction pre-processing step is usually helpful to reduce data fluctuation due to acquisition artifacts (e.g. reducing the number of misclassified voxels).
• Use Case 2: Volume rendering
  • Noise reduction will result in nicer looking volume renderings
• Use Case 3: Noise reduction as part of image processing pipeline
  • Could offer a better segmentation and classification on specific brain image analysis such as in Multiple Sclerosis lesion segmentation

• 

  Raw T1 weighted MRI Image

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

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

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  DTI-FA map without image filtering process

• 

  DTI-FA map with AAD image filtering (q=0.4)

Similar Extensions

• Gradient Anisotropic Diffusion

References

• 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.
• Filho, A.C. da S.S. et al., 2014. Brain Activation Inhomogeneity Highlighted by the Isotropic Anomalous Diffusion Filter. In Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Chicago: IEEE, pp. 3313–3316.
• Senra Filho, A.C. da S., Duque, J.J. & Murta, L.O., 2013. Isotropic anomalous filtering in Diffusion-Weighted Magnetic Resonance Imaging. I. E. in M. and B. Society, ed. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 2013, pp.4022–5.

Information for Developers

Repositories:

• Source code: GitHub repository
• Issue tracker: open issues and enhancement requests