Documentation/Nightly/Extensions/DTIAtlasFiberAnalyzer - Revision history

Fbudin at 22:48, 11 December 2014

2014-12-11T22:48:01Z

Fbudin at 22:47, 11 December 2014

2014-12-11T22:47:22Z

Fbudin at 17:55, 9 September 2013

2013-09-09T17:55:28Z

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

2013-06-14T07:56:02Z

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

Fbudin: /* Quick Tour of Features and Use */

2013-01-17T22:23:03Z

Quick Tour of Features and Use

Fbudin: Created page with 'NOTOC {{documentation/{{documentation/version}}/module-header}} {{documentation/{{documentation/v…'

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

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Francois Budin 
Contributors: Jean-Baptiste Berger (NIRAL, University of North Carolina), Clement Vachet (SCI Institute, University of Utah), Francois Budin (NIRAL, University of North Carolina), Martin Styner (NIRAL, University of North Carolina) 
Contact: Francois Budin, <email>fbudin@unc.edu</email> 
Website: http://www.nitrc.org/projects/fvlight/ 
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}}

===Module Description===
{| style="color:green" border="1"
|Program title || DTI Atlas Fiber Analyzer
|-
|Program description ||
Compute statistics on DTI Fiber Tracts. Writing a data parameter file : The file need a special key in the first line which is : "Data parameters for DTIAtlasFiberAnalyzer : ". Each line after the first line need a key and then the value. For the CSV file, write the key : "CSVFile : " and the path of your file. For the Data column, write the key : "Data Column : " and the number of the column in the CSV File. For the Deformation Field column, write the key : "Defomation Field Column : " and the number of the column in the CSV File. If you don't put this line, the software will use no deformations field. For the Case column, write the key : "Case Column : " and the number of the column in the CSV File. If you don't put this line, the software will use the name of the T1 image. For the Output folder, write the key : "Output Folder : " and the path of your file. Writting an analysis file : The file need a special key in the first line which is : "Analysis parameters for DTIAtlasFiberAnalyzer : ". Each line after the first line need a key and then the value. For the Atlas folder, write the key : "Atlas Fiber Folder : " and path to the folder. To choose the selected fibers use the key : "Selected Fibers : " followed by the name of each fibers separated by a coma. As for the fibers, you can choose selected planes thanks to the key : "Selected Planes : ". To specify which parameters you want to use, write the key : "Profile parameter : " followed by each parameters separated by a coma (fa,md,fro,ad,l2,l3,ga,rd). Then with the key : "Col and Row : " followed by "Case in row" or "Case in column" you can select the layout of the datasheet. Finally, "Auto Plane Origin : " followed either by "median" or "cog" will define the way to calculate an eventual auto plane origin.

|-
|Program version ||
|-
|Program documentation-url ||
|-
|}

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them.
{|
|
'''''DTIAtlasFiberAnalyzer Command Line Parameters''''': Command Line Parameters for DTIAtlasFiberAnalyzer, use only with the option nogui
* '''nogui''' [--nogui] : If this option is used, you will use the command line, DEFAULT=false ''Default value: false''
* '''datafile''' [--datafile] [-D]: File containing the Data parameters for DTIAtlasFiberAnalyzer
* '''analysisfile''' [--analysisfile] [-A]: File containing the Analysis parameters for DTIAtlasFiberAnalyzer
* '''loadCSV''' [--loadCSV] [-L]: Load a CSV file with this filename. Default: no file, the software takes the one from the parameters file.
* '''debug''' [--debug] : debug for computer scientist DEFAULT=false ''Default value: false''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

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 Contact: Francois Budin, <email>fbudin@unc.edu</email><br>
 Website: http://www.nitrc.org/projects/fvlight/<br>
-License: [http://www.nitrc.org/include/glossary.php#187 http://www.apache.org/licenses/LICENSE-2.0]
+License: [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]
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 Image:UNC-NIRAL.png‎|NIRAL

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 Contact: Francois Budin, <email>fbudin@unc.edu</email><br>
 Website: http://www.nitrc.org/projects/fvlight/<br>
-License: [http://www.nitrc.org/include/glossary.php#187 BSD]
+License: [http://www.nitrc.org/include/glossary.php#187 http://www.apache.org/licenses/LICENSE-2.0]
 <gallery>
 Image:UNC-NIRAL.png‎|NIRAL

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		+	Image:DTIAtlasFiberAnalyzerGenu profile FA.png\|Genu - FA profile
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 * <span style="color:green">'''loadCSV'''</span> [<span style="color:orange">--loadCSV</span>] [<span style="color:pink">-L</span>]: Load a CSV file with this filename. Default: no file, the software takes the one from the parameters file.
 * <span style="color:green">'''debug'''</span> [<span style="color:orange">--debug</span>] : debug for computer scientist DEFAULT=false ''Default value: false''
-|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
+|[[Image:Screenshot-DTI Atlas Fiber Analyser.png|thumb|280px|User Interface]]
 |}