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

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{{ambox
 
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| type  = protection
 
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| image = [[File:InProgress.png|40px|alt=Work in progress]]
 
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| text  = WARNING: This page is Work in Progress, which means:
 
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* the information is not complete
 
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* some information refers to other modules/extensions
 
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
 
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Author: Casey Goodlett<br>
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Author: Francois Budin<br>
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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)<br>
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Contributors: Casey Goodlett (Kitware), 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)<br>
 
Contact: Francois Budin, <email>fbudin@unc.edu</email><br>
 
Contact: Francois Budin, <email>fbudin@unc.edu</email><br>
 
Website: http://www.nitrc.org/projects/dtiprocess/<br>
 
Website: http://www.nitrc.org/projects/dtiprocess/<br>
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License: [http://www.nitrc.org/include/glossary.php#187 BSD]
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License: [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]
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<gallery>
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Image:DTIProcessLogo.png|DTIProcess
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Image:UNC-NIRAL.png‎|NIRAL
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Image:UNC-logo.png|UNC
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Image:Logo-namic.jpg‎|NAMIC
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}
 
{{documentation/{{documentation/version}}/extension-section|Extension Description}}
 
DTIProcess is a DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include:
 
DTIProcess is a DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include:
  
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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.
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* dtiestim (in Diffusion/Diffusion Weighted Images): 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.
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* dtiprocess: tool that handles tensor fields
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* dtiprocess (in Diffusion/Diffusion Tensor Images): 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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* dtiaverage (in Diffusion/Diffusion Tensor Images/CommandLineOnly): program that allows to compute the average of an arbitrary number of tensor fields. This tools should be used in a command line.
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* fibertrack: program that implements a simple streamline tractography method based on the principal eigenvector of the tensor field
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* fiberprocess (in Diffusion/Tractography): tool that manage fiber files extracted from the fibertrack tool or any fiber tracking algorithm
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* fiberprocess: tool that manage fiber files extracted from the fibertrack tool or any fiber tracking algorithm
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* fiberstats (in Diffusion/Tractography/CommandLineOnly): program that prints out some statistics computed on a fiber bundle. This tools should be used in a command line.
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* A couple other tools that are included in the package and that are not CLI compatible
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NOTE:
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* maxcurvature, scalartransform and fibertrack are not packaged anymore as part of the DTIProcess Slicer extension. Those tools are not maintained anymore.
  
 
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{{documentation/{{documentation/version}}/extension-section|Modules}}
 
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*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
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*[[Documentation/{{documentation/version}}/Modules/dtiestim|dtiestim]]
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*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
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*[[Documentation/{{documentation/version}}/Modules/dtiprocess|dtiprocess]]
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*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]]
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*[[Documentation/{{documentation/version}}/Modules/dtiaverage|dtiaverage]]
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*[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]]
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*[[Documentation/{{documentation/version}}/Modules/fiberprocess|fiberprocess]]
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*[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]]
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*[[Documentation/{{documentation/version}}/Modules/fiberstats|fiberstats]]
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*[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]]
 
  
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{{documentation/{{documentation/version}}/extension-section|Deprecated tools (used to be part of this package)}}
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*[[Documentation/{{documentation/version}}/Modules/fibertrack|fibertrack]]
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*[[Documentation/{{documentation/version}}/Modules/maxcurvature|maxcurvature]]
 
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{{documentation/{{documentation/version}}/extension-section|Use Cases}}
 
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[http://plastimatch.org/data_sources.html Sample data] to use with modules.
 
 
<gallery widths="200px" perrow="4">
 
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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:FiberStats-Results.png |Fibers statistics
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Image:after_reg.png|After Registration
 
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{{documentation/{{documentation/version}}/extension-section|Tutorials}}
 
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<gallery widths="200px" perrow="4">
 
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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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Image:fixed.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]
 
 
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{{documentation/{{documentation/version}}/extension-section|References}}
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{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
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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.
 
−
* 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.
 
−
* 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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{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
 
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{{documentation/{{documentation/version}}/extension-developerinfo}}
 
  
 
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Latest revision as of 19:05, 16 July 2014

Home < Documentation < Nightly < Extensions < DTIProcess


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


Introduction and Acknowledgements

Author: Francois Budin
Contributors: Casey Goodlett (Kitware), 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)
Contact: Francois Budin, <email>fbudin@unc.edu</email>
Website: http://www.nitrc.org/projects/dtiprocess/
License: Apache License, Version 2.0

  • DTIProcess

  • NIRAL

  • UNC

  • NAMIC

Extension Description

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

  • dtiestim (in Diffusion/Diffusion Weighted Images): 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 (in Diffusion/Diffusion Tensor Images): tool that handles tensor fields
  • dtiaverage (in Diffusion/Diffusion Tensor Images/CommandLineOnly): program that allows to compute the average of an arbitrary number of tensor fields. This tools should be used in a command line.
  • fiberprocess (in Diffusion/Tractography): tool that manage fiber files extracted from the fibertrack tool or any fiber tracking algorithm
  • fiberstats (in Diffusion/Tractography/CommandLineOnly): program that prints out some statistics computed on a fiber bundle. This tools should be used in a command line.

NOTE:

  • maxcurvature, scalartransform and fibertrack are not packaged anymore as part of the DTIProcess Slicer extension. Those tools are not maintained anymore.

Modules

Deprecated tools (used to be part of this package)

Use Cases

  • Baseline Image

  • iDWI

  • Fractional Anisotropy

  • Mean Diffusivity

  • 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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