Documentation/Nightly/Extensions/PBNRR

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Introduction and Acknowledgements

Extension: Physics-Based Non-Rigid Registration (PBNRR) Acknowledgments: This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment. Author: Fotis Drakopoulos Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC) Contact: Nikos Chrisochoides, <email>npchris@gmail.com</email> Website: https://crtc.cs.odu.edu/joomla/ License: BSD

Center for Real-time Computing

Module Description

The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.

Use Cases

Case1 Input; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.

Case1 Output; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.

Case2 Input; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.

Case2 Output; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.

Panels and their use

Registration Parameters: Block Radius: Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1). Window Radius: Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5). Selection Fraction: Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05). Rejection Fraction: Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25). Outlier Rejection Steps: Number of outlier rejection steps. Value should be between [1,20] (default: 5). Interpolation Steps: Number of interpolation steps. Value should be between [1,20] (default: 5). Young Modulus: Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2). Poisson Ratio: Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45). Input/Output: Moving Image: The input moving image. Fixed Image: The input moving image. Mask Image: The input moving image. Mesh: The input moving image. Output Volume: Moving image to the fixed image coordinate frame (optional). Output Direct Deformation Field: Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional). Output Inverse Deformation Field: Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional). Output Warped Mesh: The warped tetrahedral mesh in vtk file format (optional).

PBNRR UI

References

• Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
• Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.