View source for Modules:BRAINSROIAuto

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__NOTOC__
===Module Name===
BRAINSROIAuto

{|
|[[Image:BRAINSRROIAutoUI.png|thumb|280px|User Interface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation


===Authors, Collaborators & Contact===

Author: Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu

Contributors: Hans Johnson(1,3,4);  (1=University of Iowa Department of Psychiatry,  3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering)  

===Module Description===

{| style="color:green" border="1"

|Program title || BRAINSROIAuto - Foreground masking tool

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|Program version || 2.4.1

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|Program documentation-url || 
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== Usage ==
BRAINSROIAuto finds the foreground tissue region in an image.

* <span style="color:blue">'''''IO''''' </span> 
** <span style="color:green">'''Input Image Volume'''</span> [<span style="color:orange">--inputVolume</span>] : The input image for finding the largest region filled mask.
** <span style="color:green">'''Output Mask'''</span> [<span style="color:orange">--outputROIMaskVolume</span>] : The ROI automatically found from the input image.
** <span style="color:green">'''Output Image Clipped by ROI'''</span> [<span style="color:orange">--outputClippedVolumeROI</span>] : The inputVolume clipped to the region of the brain mask.


* <span style="color:blue">'''''Configuration Parameters''''' </span> 
** <span style="color:green">'''Otsu Percentile Threshold'''</span> [<span style="color:orange">--otsuPercentileThreshold</span>] : Parameter to the Otsu threshold algorithm. ''Default value: 0.01''
** <span style="color:green">'''Otsu Correction Factor'''</span> [<span style="color:orange">--thresholdCorrectionFactor</span>] : A factor to scale the Otsu algorithm's result threshold, in case clipping mangles the image. ''Default value: 1.0''
** <span style="color:green">'''Closing Size'''</span> [<span style="color:orange">--closingSize</span>] : The Closing Size (in millimeters) for largest connected filled mask.  This value is divided by image spacing and rounded to the next largest voxel number. ''Default value: 9.0''
** <span style="color:green">''' ROIAuto Dilate Size'''</span> [<span style="color:orange">--ROIAutoDilateSize</span>] : This flag is only relavent when using ROIAUTO mode for initializing masks.  It defines the final dilation size to capture a bit of background outside the tissue region.  At setting of 10mm has been shown to help regularize a BSpline registration type so that there is some background constraints to match the edges of the head better. ''Default value: 0.0''
** <span style="color:green">'''Output Image Pixel Type'''</span> [<span style="color:orange">--outputVolumePixelType</span>] : The output image Pixel Type is the scalar datatype for representation of the Output Volume. ''Default value: short''


===Tutorials===

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

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSROIAuto depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
BRAINSROIAuto depends on BRAINSCommonLib

===Tests===
http://testing.psychiatry.uiowa.edu

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

== More Information == 

===Acknowledgment===
The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.  


===References===
Publications related to this module go here. Links to pdfs would be useful.
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