Slicer Wiki - User contributions [en]

Documentation/Nightly/Extensions/DTIAtlasBuilder

2013-02-20T21:38:26Z

Adrienkaiser:

{{documentation/{{documentation/version}}/module-header}}


{{documentation/{{documentation/version}}/module-section|Warning}}
{{documentation/{{documentation/version}}/module-developerinfo}}

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

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Adrien Kaiser 
Contact: Adrien Kaiser, <email>akaiser@unc.edu</email> 
Website: http://www.nitrc.org/projects/dtiatlasbuilder/ 
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}}

===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)
|[[Image:DTIAtlasBuilder_Interface.png|thumb|280px|User Interface]]
|}


{{documentation/{{documentation/version}}/extension-section|Screenshots}}
<gallery widths="200px" perrow="4">
Image:DTIAtlasBuilder_Interface.png|Files tab
Image:DTIAtlasBuilder_Affine.png|Affine Atlas tab
Image:DTIAtlasBuilder_Diffeo.png|Diffeomorphic Atlas tab
Image:DTIAtlasBuilder_FinalRes.png|Final Resampling tab
Image:DTIAtlasBuilder_SoftConfig.png|Software Configuration tab
Image:DTIAtlasBuilder_GridProc.png|Grid Processing tab
</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/dtiatlasbuilder/


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

File:DTIAtlasBuilder GridProc.png

2013-02-20T21:34:29Z

Adrienkaiser:

File:DTIAtlasBuilder SoftConfig.png

2013-02-20T21:34:15Z

Adrienkaiser:

File:DTIAtlasBuilder FinalRes.png

2013-02-20T21:33:58Z

Adrienkaiser:

File:DTIAtlasBuilder Diffeo.png

2013-02-20T21:33:33Z

Adrienkaiser:

File:DTIAtlasBuilder Affine.png

2013-02-20T21:32:58Z

Adrienkaiser:

Documentation/Nightly/Extensions/DTIAtlasBuilder

2013-02-20T21:28:12Z

Adrienkaiser:

{{documentation/{{documentation/version}}/module-header}}


{{documentation/{{documentation/version}}/module-section|Warning}}
{{documentation/{{documentation/version}}/module-developerinfo}}

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

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Adrien Kaiser 
Contact: Adrien Kaiser, <email>akaiser@unc.edu</email> 
Website: http://www.nitrc.org/projects/dtiatlasbuilder/ 
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}}

===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)
|[[Image:DTIAtlasBuilder_Interface.png|thumb|280px|User Interface]]
|}


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:DTIAtlasBuilder_Interface.png|User Interface
</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/dtiatlasbuilder/


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

Documentation/Nightly/Extensions/DTIAtlasBuilder

2013-02-20T21:27:41Z

Adrienkaiser:

{{documentation/{{documentation/version}}/module-header}}


{{documentation/{{documentation/version}}/module-section|Warning}}
{{documentation/{{documentation/version}}/module-developerinfo}}

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

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Adrien Kaiser 
Contact: Adrien Kaiser, <email>akaiser@unc.edu</email> 
Website: http://www.nitrc.org/projects/dtiatlasbuilder/ 
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}}

===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)
|[[Image:DTIAtlasBuilder_Interface.png|thumb|280px|User Interface]]
|}


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:DTIAtlasBuilder_Interface.png|User Interface
</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/dtiatlasbuilder/


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

File:DTIAtlasBuilder Interface.png

2013-02-20T21:26:26Z

Adrienkaiser:

Documentation/Nightly/Extensions/DTIAtlasBuilder

2013-02-20T21:25:45Z

Adrienkaiser:

{{documentation/{{documentation/version}}/module-header}}


{{documentation/{{documentation/version}}/module-section|Warning}}
{{documentation/{{documentation/version}}/module-developerinfo}}

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

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Adrien Kaiser 
Contact: Adrien Kaiser, <email>akaiser@unc.edu</email> 
Website: http://www.nitrc.org/projects/dtiatlasbuilder/ 
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}}

===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)
|[[Image:DTIPrep-Extension-GUI.png|thumb|280px|User Interface]]
|}


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:DTIPrep-Extension-GUI.png|DWI image loaded
Image:DTIPrep-Extension-Sphere.png|Sphere representing the gradient directions
</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/dtiatlasbuilder/


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

Documentation/Nightly/Extensions

2013-02-20T21:11:08Z

Adrienkaiser:

<noinclude>{{:{{FULLPAGENAME}}/Description}}

__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|CARMA]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

Documentation/Nightly/Extensions/DTIAtlasBuilder

2013-02-20T21:10:47Z

Adrienkaiser: Created page with 'test'

test