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

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{{documentation/{{documentation/version}}/module-section|Warning}}
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{{documentation/{{documentation/version}}/module-developerinfo}}
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This extension currently does not work in Slicer4 nightly build on Windows and Mac. This should be corrected soon.
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Author: Adrien Kaiser<br>
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Contact: Adrien Kaiser, <email>akaiser@unc.edu</email><br>
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Website: http://www.nitrc.org/projects/dtiatlasbuilder/<br>
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License: [http://www.nitrc.org/include/glossary.php#187 BSD]
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<gallery>
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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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</gallery>
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}
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===Quick Tour of Features and Use===
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This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps :
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- Affine Registration with BRAINSFit
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- Non Linear Registration with AtlasWerks
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A final step will apply the transformations to the original DTI images so that the final average can be computed.
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The main function writes a python script that will be executed to compute the Atlas.
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By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI.
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Using the GUI, you will be able to save or load a dataset file or a parameter file.
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--overwrite
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    If you want to overwrite on previous compute (default: 0)
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  --nogui
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    If you do not need the GUI (default: 0)
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{|
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* <span style="color:blue">'''''Parameters'''''</span>:
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** <span style="color:green">'''Parameter File'''</span> [<span style="color:orange">--parameter_file</span>] [<span style="color:pink">-p</span>]: Parameter file created with this program (.txt)
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** <span style="color:green">'''Dataset File'''</span> [<span style="color:orange">--dataset_file</span>] [<span style="color:pink">-d</span>]: CSV file containing the dataset (.csv)
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** <span style="color:green">'''Configuration file'''</span> [<span style="color:orange">--configuration_file</span>] [<span style="color:pink">-c</span>]: Software configuration file
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** <span style="color:green">'''Overwrite'''</span> [<span style="color:orange">--overwrite</span>]: If you want to overwrite on previous compute (default: 0)
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** <span style="color:green">'''No GUI'''</span> [<span style="color:orange">--nogui</span>] : If you do not need the GUI (default: 0)
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|[[Image:DTIPrep-Extension-GUI.png|thumb|280px|User Interface]]
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|}
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{{documentation/{{documentation/version}}/extension-section|Use Cases}}
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<gallery widths="200px" perrow="4">
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Image:DTIPrep-Extension-GUI.png|DWI image loaded
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Image:DTIPrep-Extension-Sphere.png|Sphere representing the gradient directions
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</gallery>
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{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
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N/A
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{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
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More information as well as the source code can found on the project webpage: http://www.nitrc.org/projects/dtiatlasbuilder/
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{{documentation/{{documentation/version}}/extension-footer}}
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Revision as of 21:25, 20 February 2013

Home < Documentation < Nightly < Extensions < DTIAtlasBuilder

Warning

Work in progress
 Section under construction.


This extension currently does not work in Slicer4 nightly build on Windows and Mac. This should be corrected soon.

Introduction and Acknowledgements

Author: Adrien Kaiser
Contact: Adrien Kaiser, <email>akaiser@unc.edu</email>
Website: http://www.nitrc.org/projects/dtiatlasbuilder/
License: BSD

  • NIRAL

  • UNC

  • NAMIC

Extension Description

Quick Tour of Features and Use

This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps : - Affine Registration with BRAINSFit - Non Linear Registration with AtlasWerks A final step will apply the transformations to the original DTI images so that the final average can be computed.

The main function writes a python script that will be executed to compute the Atlas.

By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a parameter file. 

--overwrite
    If you want to overwrite on previous compute (default: 0)

  --nogui
    If you do not need the GUI (default: 0)
  • Parameters:
    • Parameter File [--parameter_file] [-p]: Parameter file created with this program (.txt)
    • Dataset File [--dataset_file] [-d]: CSV file containing the dataset (.csv)
    • Configuration file [--configuration_file] [-c]: Software configuration file
    • Overwrite [--overwrite]: If you want to overwrite on previous compute (default: 0)
    • No GUI [--nogui] : If you do not need the GUI (default: 0)
User Interface


Use Cases

  • DWI image loaded

  • Sphere representing the gradient directions

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/dtiatlasbuilder/

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