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

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<noinclude>{{documentation/versioncheck}}</noinclude>
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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.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]
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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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{|
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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 (.txt)
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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:DTIAtlasBuilder_Interface.png|thumb|280px|User Interface]]
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|}
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{{documentation/{{documentation/version}}/extension-section|Screenshots}}
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<gallery widths="200px" perrow="4">
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Image:DTIAtlasBuilder_Interface.png|Files tab
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Image:DTIAtlasBuilder_Affine.png|Affine Atlas tab
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Image:DTIAtlasBuilder_Diffeo.png|Diffeomorphic Atlas tab
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Image:DTIAtlasBuilder_FinalRes.png|Final Resampling tab
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Image:DTIAtlasBuilder_SoftConfig.png|Software Configuration tab
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Image:DTIAtlasBuilder_GridProc.png|Grid Processing tab
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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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Latest revision as of 22:49, 11 December 2014

Home < Documentation < Nightly < Extensions < DTIAtlasBuilder


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


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: Apache License, Version 2.0

  • 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.

  • 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 (.txt)
    • 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


Screenshots

  • Files tab

  • Affine Atlas tab

  • Diffeomorphic Atlas tab

  • Final Resampling tab

  • Software Configuration tab

  • Grid Processing tab

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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