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

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* dtiestim: tool that takes in a set of DWIs in nrrd format and estimates a tensor field out of it. It also has many useful options.
 
* dtiestim: tool that takes in a set of DWIs in nrrd format and estimates a tensor field out of it. It also has many useful options.
 
* dtiprocess: tool that handles tensor fields
 
* dtiprocess: tool that handles tensor fields
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* dtiaverage: program that allows to compute the average of an arbitrary number of tensor fields
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* maxcurvature: computes Hessian of an image. Typically the input image is a Fractional Anisotropy (FA) image
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* dtiaverage (Should be used in a command line): program that allows to compute the average of an arbitrary number of tensor fields
 
* fibertrack: program that implements a simple streamline tractography method based on the principal eigenvector of the tensor field
 
* fibertrack: program that implements a simple streamline tractography method based on the principal eigenvector of the tensor field
 
* fiberprocess: tool that manage fiber files extracted from the fibertrack tool or any fiber tracking algorithm
 
* fiberprocess: tool that manage fiber files extracted from the fibertrack tool or any fiber tracking algorithm
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* fiberstats: program that prints out some statistics computed on a fiber bundle
 
* A couple other tools that are included in the package and that are not CLI compatible
 
* A couple other tools that are included in the package and that are not CLI compatible
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All the above software will appear in 3D Slicer in the module list under '''Diffusion>NIRALPipeline'''
  
 
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*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
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*[[Documentation/{{documentation/version}}/Modules/dtiprocess|dtiprocess]]
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*[[Documentation/{{documentation/version}}/Modules/dtiaverage|dtiaverage]]
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*[[Documentation/{{documentation/version}}/Modules/fibertrack|fibertrack]]
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*[[Documentation/{{documentation/version}}/Modules/fiberprocess|fiberprocess]]
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*[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
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*[[Documentation/{{documentation/version}}/Modules/fiberstats|fiberstats]]
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*[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]]
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*[[Documentation/{{documentation/version}}/Modules/maxcurvature|maxcurvature]]
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[http://plastimatch.org/data_sources.html Sample data] to use with modules.
 
[http://plastimatch.org/data_sources.html Sample data] to use with modules.
 
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Image:plastimatch_dicomrt_ss.png|DICOM-RT Structure Set
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Image:DTIEstim-B0-crop.png|Baseline Image
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Image:plastimatch_dicomrt_dose.png|DICOM-RT Dose
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Image:DTIestim-iDWI-sagittal.png|iDWI
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Image:plastimatch_image_1.png|Before Registration
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Image:DTIEstim-DTI-FA-crop.png|Fractional Anisotropy
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Image:plastimatch_image_2.png|After Registration
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Image:DTIProcess-MD-crop.png|Mean Diffusivity
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Image:before_reg.png|Before Registration
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Image:FiberTrack-fibers.png|Fiber tractography
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Image:after_reg.png|After Registration
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Image:FiberStats-Results.png |Fibers statistics
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Image:plastimatch_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1023/3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]
 
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Image:plastimatch_tutorial_data.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1004/rider-lung-images.tar.gz Download tutorial data]
 
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Image:plastimatch_dicomrt_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1568/3D_Slicer_Plastimatch_DICOM_RT_Tutorial_2010_12_28.pdf Download tutorial (PDF)]
 
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Image:plastimatch_dicomrt_ss.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz (Download tutorial data)]
 
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Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]
 
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* G Sharp, N Kandasamy, H Singh, M Folkert, "GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration," Physics in Medicine and Biology, 52(19), pp 5771-83, 2007.
 
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* V Boldea, G Sharp, SB Jiang, D Sarrut, "4D-CT lung motion estimation with deformable registration: Quantification of motion nonlinearity and hysteresis," Medical Physics, 33(3), pp 1008-18, 2008.
 
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* Z Wu, E Rietzel, V Boldea, D Sarrut, G Sharp, "Evaluation of deformable registration of patient lung 4DCT with sub-anatomical region segmentations," Medical Physics, 35(2), pp 775-81, 2008.
 
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* G Sharp et al. "Plastimatch - An open source software suite for radiotherapy image processing," Proceedings of the XVIth International Conference on the use of Computers in Radiotherapy, May, 2010.
 
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* N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.
 
  
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More information as well as the source code can found on the project webpage: http://www.nitrc.org/projects/dtiprocess
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Revision as of 14:49, 29 November 2012

Home < Documentation < Nightly < Extensions < DTIProcess

Introduction and Acknowledgements

Author: Casey Goodlett
Contributors: Aditya Gupta (NIRAL, University Of North Carolina), Clement Vachet (SCI Institute, University of Utah), Francois Budin (NIRAL, University of North Carolina), Guido Gerig (SCI Institute, University of Utah), Hans Johnson (University of Iowa), Martin Styner (NIRAL, University Of North Carolina), Sylvain Gouttard (SCI Institute, University of Utah), Yundi Shi (NIRAL, University of North Carolina), Zhexing Liu (NIRAL, University of North Carolina), Casey Goodlett (Kitware)
Contact: Francois Budin, <email>fbudin@unc.edu</email>
Website: http://www.nitrc.org/projects/dtiprocess/
License: BSD


Extension Description

DTIProcess is a DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include:

  • dtiestim: tool that takes in a set of DWIs in nrrd format and estimates a tensor field out of it. It also has many useful options.
  • dtiprocess: tool that handles tensor fields
  • maxcurvature: computes Hessian of an image. Typically the input image is a Fractional Anisotropy (FA) image
  • dtiaverage (Should be used in a command line): program that allows to compute the average of an arbitrary number of tensor fields
  • fibertrack: program that implements a simple streamline tractography method based on the principal eigenvector of the tensor field
  • fiberprocess: tool that manage fiber files extracted from the fibertrack tool or any fiber tracking algorithm
  • fiberstats: program that prints out some statistics computed on a fiber bundle
  • A couple other tools that are included in the package and that are not CLI compatible

All the above software will appear in 3D Slicer in the module list under Diffusion>NIRALPipeline

Modules

Use Cases

Sample data to use with modules.

  • Baseline Image

  • iDWI

  • Fractional Anisotropy

  • Mean Diffusivity

  • Fiber tractography

  • Fibers statistics

Similar Extensions

N/A

Information for Developers

More information as well as the source code can found on the project webpage: http://www.nitrc.org/projects/dtiprocess

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