Documentation/Nightly/Extensions/DTIAtlasBuilder - Revision history

Fbudin at 22:49, 11 December 2014

2014-12-11T22:49:12Z

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T08:00:21Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

Adrienkaiser at 21:38, 20 February 2013

2013-02-20T21:38:26Z

Adrienkaiser at 21:28, 20 February 2013

2013-02-20T21:28:12Z

Adrienkaiser at 21:27, 20 February 2013

2013-02-20T21:27:41Z

Adrienkaiser at 21:25, 20 February 2013

2013-02-20T21:25:45Z

Adrienkaiser: Created page with 'test'

2013-02-20T21:10:47Z

Created page with 'test'

New page

test

@@ Line 13: / Line 13: @@
 Contact: Adrien Kaiser, <email>akaiser@unc.edu</email><br>
 Website: http://www.nitrc.org/projects/dtiatlasbuilder/<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

← Older revision		Revision as of 08:00, 14 June 2013
Line 1:		Line 1:
		+	<noinclude>{{documentation/versioncheck}}</noinclude>
	<!-- ---------------------------- -->		<!-- ---------------------------- -->
	{{documentation/{{documentation/version}}/module-header}}		{{documentation/{{documentation/version}}/module-header}}

@@ Line 46: / Line 46: @@
 <!-- ---------------------------- -->
-{{documentation/{{documentation/version}}/extension-section|Use Cases}}
+{{documentation/{{documentation/version}}/extension-section|Screenshots}}
 <gallery widths="200px" perrow="4">
-Image:DTIAtlasBuilder_Interface.png|User Interface
+Image:DTIAtlasBuilder_Interface.png|Files tab
 </gallery>

@@ Line 32: / Line 32: @@
 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.
 {|
@@ Line 44: / Line 38: @@
 ** <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)
 ** <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)
-** <span style="color:green">'''Configuration file'''</span> [<span style="color:orange">--configuration_file</span>] [<span style="color:pink">-c</span>]: Software configuration file
+** <span style="color:green">'''Configuration file'''</span> [<span style="color:orange">--configuration_file</span>] [<span style="color:pink">-c</span>]: Software configuration file (.txt)
 ** <span style="color:green">'''Overwrite'''</span> [<span style="color:orange">--overwrite</span>]: If you want to overwrite on previous compute (default: 0)
 ** <span style="color:green">'''No GUI'''</span> [<span style="color:orange">--nogui</span>] : If you do not need the GUI (default: 0)

@@ Line 47: / Line 47: @@
 ** <span style="color:green">'''Overwrite'''</span> [<span style="color:orange">--overwrite</span>]: If you want to overwrite on previous compute (default: 0)
 ** <span style="color:green">'''No GUI'''</span> [<span style="color:orange">--nogui</span>] : If you do not need the GUI (default: 0)
-|[[Image:DTIPrep-Extension-GUI.png|thumb|280px|User Interface]]
+|[[Image:DTIAtlasBuilder_Interface.png|thumb|280px|User Interface]]
 |}
@@ Line 54: / Line 54: @@
 {{documentation/{{documentation/version}}/extension-section|Use Cases}}
 <gallery widths="200px" perrow="4">
-Image:DTIPrep-Extension-GUI.png|DWI image loaded
+Image:DTIAtlasBuilder_Interface.png|User Interface
 </gallery>

← Older revision		Revision as of 21:25, 20 February 2013
Line 1:		Line 1:
−	~~test~~	+	<!-- ---------------------------- -->
		+	{{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<br>
		+	Contact: Adrien Kaiser, <email>akaiser@unc.edu</email><br>
		+	Website: http://www.nitrc.org/projects/dtiatlasbuilder/<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}}
		+
		+	===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)
		+
		+	{\|
		+	\|
		+	* <span style="color:blue">'''''Parameters'''''</span>:
		+	** <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)
		+	** <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)
		+	** <span style="color:green">'''Configuration file'''</span> [<span style="color:orange">--configuration_file</span>] [<span style="color:pink">-c</span>]: Software configuration file
		+	** <span style="color:green">'''Overwrite'''</span> [<span style="color:orange">--overwrite</span>]: If you want to overwrite on previous compute (default: 0)
		+	** <span style="color:green">'''No GUI'''</span> [<span style="color:orange">--nogui</span>] : 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}}
		+	<!-- ---------------------------- -->