PBNRR Slicer Extension

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 the NSF grant CCF-1439079 and by the John Simon Guggenheim Foundation and the Richard T. Cheng Endowment.

Contributors: Angelos Angelopoulos (CRTC), Fotis Drakopoulos (CRTC, author of PBNRR), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)

Contact: Nikos Chrisochoides

Website: https://crtc.cs.odu.edu/

License: BSD

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.

Parameters

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 Parameters

Input Moving Image: The input moving image (preoperative).
Input Fixed Image: The input fixed image (intraoperative).
Input Mask Image: The input moving mask.
Input Mesh: The input mesh.
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).

References

Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005.
Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033

History

The module was originally hosted at https://github.com/fdrakopo/PBNRR_SlicerExtension and maintained by Fotis Drakopoulos from the Center for Real-Time Computing (CRTC).

On August 1st 2018, associated files have been added to https://github.com/aangelos28/PBNRR maintained by Angelos Angelopoulos also from the Center for Real-Time Computing (CRTC). Previous commit history was ignored because it was short (only few commits) and it contained large data files causing the initial checkout to take a long time.