Difference between revisions of "Documentation/Nightly/Extensions/PBNRR"

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Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]<br>
 
Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]<br>
 
Acknowledgments:
 
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.<br>
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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.<br>
 +
 
 +
Maintainer: Angelos Angelopoulos (CRTC)<br>
 
Author: Fotis Drakopoulos<br>
 
Author: Fotis Drakopoulos<br>
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Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)<br>
+
Contributors: Angelos Angelopoulos (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)<br>
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Contact: Nikos Chrisochoides, <email>npchris@gmail.com</email><br>
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Contact: Nikos Chrisochoides (<email>npchris@gmail.com</email>), Angelos Angelopoulos, (<email>aangelos28@gmail.com</email>)<br>
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Website: https://crtc.cs.odu.edu/joomla/<br>
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Website: https://crtc.cs.odu.edu/<br>
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License: BSD<br>
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License: BSD
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|Image:CRTC_logo.jpg|Center for Real-time Computing  
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|Image:Crtc_logo.png|Center for Real-time Computing  
 
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{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
{|
 
{|
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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.]]
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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.]]
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|[[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: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.]]
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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.]]
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|[[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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|[[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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|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
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* '''Registration Parameters:'''
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** '''Block Radius:'''  Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).
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** '''Window Radius:'''  Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).
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** '''Selection Fraction:'''  Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).
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** '''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).
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** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).
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** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).
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** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).
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** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).
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* '''Input/Output:'''
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** '''Input Moving Image:''' The input moving image (preoperative).
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** '''Input Fixed Image:''' The input fixed image (intraoperative).
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** '''Input Mask Image:''' The input moving mask.
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** '''Input Mesh:''' The input mesh.
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** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).
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** '''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).
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** '''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).
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** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).
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|[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]
 
|}
 
|}
  
 
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
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{{documentation/{{documentation/version}}/module-section|References}}
 
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* Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
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* 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.  
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* 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.
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* 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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Latest revision as of 14:15, 7 August 2018

Home < Documentation < Nightly < Extensions < PBNRR


For the latest Slicer documentation, visit the read-the-docs.


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

Maintainer: Angelos Angelopoulos (CRTC)
Author: Fotis Drakopoulos
Contributors: Angelos Angelopoulos (CRTC), 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>), Angelos Angelopoulos, (<email>aangelos28@gmail.com</email>)
Website: https://crtc.cs.odu.edu/
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.

Tutorials

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:
    • 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).
PBNRR UI

Similar Modules

N/A

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

Information for Developers

Work in progress
 Section under construction.
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