View source for Documentation/Nightly/Extensions/DTIPrep

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Francois Budin<br>
Contributors: Mahshid Farzinfar (1), Zhexing Liu (1), Martin Styner(1),Hans Johnson(2,3,4), Joy Matsui(2), Kent Williams(2); (1=Department of Psychiatry, University of North Carolina at Chapel Hill, 2=University of Iowa Department of Psychiatry, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering)<br>
Contact: Francois Budin, <email>fbudin@unc.edu</email><br>
Website: http://www.nitrc.org/projects/dtiprep/<br>
License: [http://www.nitrc.org/include/glossary.php#187 BSD]
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Image:UNC-NIRAL.png‎|NIRAL
Image:UNC-logo.png|UNC
Image:Logo-namic.jpg‎|NAMIC
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===Quick Tour of Features and Use===

The DWI/DTI Quality Control Processes from dicom data to qualified dwi image.

A list panels in the interface, their features, what they mean, and how to use them.
{|
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* <span style="color:blue">'''''Input/Ouput'''''</span>: Input/output parameters
** <span style="color:green">'''DWI file'''</span> [<span style="color:orange">--DWINrrdFile</span>] [<span style="color:pink">-w</span>]: DWI file name to convert dicom image series into or to be checked (nrrd/nhdr)
** <span style="color:green">'''xml Protocol File'''</span> [<span style="color:orange">--xmlProtocol</span>] [<span style="color:pink">-p</span>]: protocol xml file containing all the parameters
** <span style="color:green">'''Result Note'''</span> [<span style="color:orange">--resultNotesFile</span>] [<span style="color:pink">-n</span>]: result notes
** <span style="color:green">'''Output Folder'''</span> [<span style="color:orange">--outputFolder</span>] [<span style="color:pink">-f</span>]: DTIPrep creates the output folder via using both absolute path (starts with "/") and relative path. The realtive path does not start with "/". If the relative path ends with "/" means that the output folder will be created in current location, otherwise the output folder will be created in the same folder as dwi image.
** <span style="color:green">'''Create Default Protocol'''</span> [<span style="color:orange">--default</span>] [<span style="color:pink">-d</span>]: create default protocol xml file
** <span style="color:green">'''Check by Protocol'''</span> [<span style="color:orange">--check</span>] [<span style="color:pink">-c</span>]: check by protocol xml file. Default operation
|[[DTIPrep-Extension-GUI.png|thumb|280px|User Interface]]
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{{documentation/{{documentation/version}}/extension-section|More Information}}

===Acknowledgment===

This work is part of the National Alliance for Medical Image Computing NAMIC, the IBIS (Infant Brain Imaging Study) Network which is NIH funded Autism Center of Excellence (HDO55741) and additional support is provided by the following grants: NIH grants P50 MH 064065, MH070890, P30 HD03110, R01 MH091645, U54 EB005149-01 (NA-MIC) , R01 NS061965, as well as by the Track-HD project funded by the CHDI/High Q Foundation.

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{{documentation/{{documentation/version}}/extension-section|Use Cases}}
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Image:DTIPrep-Extension-GUI.png|DWI image loaded
Image:DTIPrep-Extension-Sphere.png|Sphere representing the gradient directions
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{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A

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{{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/dtiprep/

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