Documentation/4.3/Extensions/DTIProcess - Revision history

Fbudin at 19:06, 16 July 2014

2014-07-16T19:06:04Z

Fbudin at 18:58, 16 July 2014

2014-07-16T18:58:53Z

UpdateBot: Nightly -> 4.3

2013-09-05T03:35:40Z

Nightly -> 4.3

New page

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Francois Budin<br>
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>
Website: http://www.nitrc.org/projects/dtiprocess/<br>
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
<gallery>
Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
</gallery>

{{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:

* 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'''


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/dtiestim|dtiestim]]
*[[Documentation/{{documentation/version}}/Modules/dtiprocess|dtiprocess]]
*[[Documentation/{{documentation/version}}/Modules/dtiaverage|dtiaverage]]
*[[Documentation/{{documentation/version}}/Modules/fibertrack|fibertrack]]
*[[Documentation/{{documentation/version}}/Modules/fiberprocess|fiberprocess]]
*[[Documentation/{{documentation/version}}/Modules/fiberstats|fiberstats]]
*[[Documentation/{{documentation/version}}/Modules/maxcurvature|maxcurvature]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:DTIEstim-B0-crop.png|Baseline Image
Image:DTIestim-iDWI-sagittal.png|iDWI
Image:DTIEstim-DTI-FA-crop.png|Fractional Anisotropy
Image:DTIProcess-MD-crop.png|Mean Diffusivity
Image:FiberTrack-fibers.png|Fiber tractography
Image:FiberStats-Results.png |Fibers statistics
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}

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


{{documentation/{{documentation/version}}/extension-footer}}

@@ Line 2: / Line 2: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-header}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
@@ Line 11: / Line 10: @@
 License: [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]
 <gallery>
 Image:UNC-NIRAL.png‎|NIRAL
 Image:UNC-logo.png|UNC

@@ Line 9: / Line 9: @@
 Contact: Francois Budin, <email>fbudin@unc.edu</email><br>
 Website: http://www.nitrc.org/projects/dtiprocess/<br>
-License: [http://www.nitrc.org/include/glossary.php#187 BSD]
+License: [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]
 <gallery>
 Image:UNC-NIRAL.png‎|NIRAL
@@ Line 19: / Line 19: @@
 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.
+* 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
+* 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
+* 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
+* 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
+* 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.
-All the above software will appear in 3D Slicer in the module list under '''Diffusion>NIRALPipeline'''
+NOTE:
 <!-- ---------------------------- -->
@@ Line 35: / Line 34: @@
 *[[Documentation/{{documentation/version}}/Modules/dtiprocess|dtiprocess]]
 *[[Documentation/{{documentation/version}}/Modules/dtiaverage|dtiaverage]]
 *[[Documentation/{{documentation/version}}/Modules/fiberprocess|fiberprocess]]
 *[[Documentation/{{documentation/version}}/Modules/fiberstats|fiberstats]]
 *[[Documentation/{{documentation/version}}/Modules/maxcurvature|maxcurvature]]
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Use Cases}}
@@ Line 47: / Line 48: @@
 Image:DTIEstim-DTI-FA-crop.png|Fractional Anisotropy
 Image:DTIProcess-MD-crop.png|Mean Diffusivity
 Image:FiberStats-Results.png |Fibers statistics
 </gallery>