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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|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/ 
License: BSD 
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{{documentation/{{documentation/version}}/module-section|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.


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{|
|[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]
|[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]
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{|
|[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]
|[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]
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* '''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:'''
** '''Input Moving Image:''' The input moving image.
** '''Input Fixed Image:''' The input moving image.
** '''Input Mask Image:''' The input moving image.
** '''Input 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).
|[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]
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{{documentation/{{documentation/version}}/module-section|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


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[[Category:Documentation/{{documentation/version}}/Modules/Registration]]

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UpdateBot: Nightly -> 4.5