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

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{{documentation/{{documentation/version}}/module-section|Warning}}
 
{{documentation/{{documentation/version}}/module-developerinfo}}
 
 
This extension currently does not work in Slicer4 nightly build. This is due to the integration of ITKv4 in Slicer4. This should be corrected soon.
 
  
 
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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>
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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Image:DTIProcessLogo.png|DTIProcess
 
Image:UNC-NIRAL.png‎|NIRAL
 
Image:UNC-NIRAL.png‎|NIRAL
 
Image:UNC-logo.png|UNC
 
Image:UNC-logo.png|UNC
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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:
  
* 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.
* dtiprocess: tool that handles tensor fields
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* dtiprocess (in Diffusion/Diffusion Tensor Images): tool that handles tensor fields
* maxcurvature: computes Hessian of an image. Typically the input image is a Fractional Anisotropy (FA) image
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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.
* dtiaverage (Should be used in a command line): program that allows to compute the average of an arbitrary number of tensor fields
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* fiberprocess (in Diffusion/Tractography): tool that manage fiber files extracted from the fibertrack tool or any fiber tracking algorithm
* fibertrack: program that implements a simple streamline tractography method based on the principal eigenvector of the tensor field
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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.
* 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'''
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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}}/Modules/dtiprocess|dtiprocess]]
 
*[[Documentation/{{documentation/version}}/Modules/dtiprocess|dtiprocess]]
 
*[[Documentation/{{documentation/version}}/Modules/dtiaverage|dtiaverage]]
 
*[[Documentation/{{documentation/version}}/Modules/dtiaverage|dtiaverage]]
*[[Documentation/{{documentation/version}}/Modules/fibertrack|fibertrack]]
 
 
*[[Documentation/{{documentation/version}}/Modules/fiberprocess|fiberprocess]]
 
*[[Documentation/{{documentation/version}}/Modules/fiberprocess|fiberprocess]]
 
*[[Documentation/{{documentation/version}}/Modules/fiberstats|fiberstats]]
 
*[[Documentation/{{documentation/version}}/Modules/fiberstats|fiberstats]]
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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]]
 
*[[Documentation/{{documentation/version}}/Modules/maxcurvature|maxcurvature]]
 
*[[Documentation/{{documentation/version}}/Modules/maxcurvature|maxcurvature]]
 
 
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{{documentation/{{documentation/version}}/extension-section|Use Cases}}
 
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Image:DTIEstim-DTI-FA-crop.png|Fractional Anisotropy
 
Image:DTIEstim-DTI-FA-crop.png|Fractional Anisotropy
 
Image:DTIProcess-MD-crop.png|Mean Diffusivity
 
Image:DTIProcess-MD-crop.png|Mean Diffusivity
Image:FiberTrack-fibers.png|Fiber tractography
 
 
Image:FiberStats-Results.png |Fibers statistics
 
Image:FiberStats-Results.png |Fibers statistics
 
</gallery>
 
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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

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

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