Difference between revisions of "2012 Summer Project Week:NiftyReg"

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__NOTOC__
 
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<gallery>
 
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Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:Nifty_reg_logo.png|NiftyReg
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 
 
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==Instructions for Use of this Template==
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== What is Niftyreg? ==
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#Please create a new wiki page with an appropriate title for your project using the convention 2012_Winter_Project_Week:<Project Name>
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* Light-weight package for medical image registration.
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#Copy the entire text of this page into the page created above
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* Global (rigid/affine) registration based on a block-matching technique.
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#Link the created page into the list of projects for the project event
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* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
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#Delete this section from the created page
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* Implementation: C/C++ [SIMD, OpenMP, CUDA]
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
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* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
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* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
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* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>
  
 
==Key Investigators==
 
==Key Investigators==
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<h3>Objective</h3>
 
<h3>Objective</h3>
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NiftyReg is an open-source package for rigid, affine and non-linear registration developed by the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, London, UK.
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[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.
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The objective is to make NiftyReg available in Slicer.
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
  
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* The NRRD file format have been integrated into the NiftyReg package to ease its integration.
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* The XML file for one of the executable of NiftyReg: reg_aladin has been created and the slicer module created.
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* reg_aladin is the global registration tool from NiftyReg. It is based on a block-matching approach to establish correspondences and a trimmed least square optimisation to determine the robust global transformation.
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* The project CMake organisation has been altered to enable easy integration of the other executables.
  
 
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==Delivery Mechanism==
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== Reg_aladin Module screenshot==
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[[File:NiftyRegExtension_reg_aladin_module.png|800 px]]
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This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
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[[file:ExtensionManager_NiftyReg.png|400]]
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#ITK Module
 
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#Slicer Module -
 
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##Built-in -
 
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##Extension -- commandline YES
 
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##Extension -- loadable
 
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#Other (Please specify)
 
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==References==
 
==References==

Latest revision as of 14:22, 22 June 2012

Home < 2012 Summer Project Week:NiftyReg

What is Niftyreg?

  • Light-weight package for medical image registration.
  • Global (rigid/affine) registration based on a block-matching technique.
  • Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
  • Implementation: C/C++ [SIMD, OpenMP, CUDA]
  • All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
  • Installation through CMake and step-by-step install can be found here
  • Trunk can be downloaded through svn: svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg

Key Investigators

  • University College London: Marc Modat
  • BWH: Sonia Pujol

Objective

NiftyReg is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.



Approach, Plan

Our approach is to develop a CLI module for NiftyReg in Slicer4.


Progress

  • The NRRD file format have been integrated into the NiftyReg package to ease its integration.
  • The XML file for one of the executable of NiftyReg: reg_aladin has been created and the slicer module created.
  • reg_aladin is the global registration tool from NiftyReg. It is based on a block-matching approach to establish correspondences and a trimmed least square optimisation to determine the robust global transformation.
  • The project CMake organisation has been altered to enable easy integration of the other executables.

Reg_aladin Module screenshot

NiftyRegExtension reg aladin module.png 400

References

  • Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
  • Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
  • Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150
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