Modules:BRAINSROIAuto-Documentation-3.6 - Revision history

KentWilliams at 15:37, 7 May 2010

2010-05-07T15:37:03Z

KentWilliams at 15:34, 7 May 2010

2010-05-07T15:34:40Z

KentWilliams at 20:18, 6 May 2010

2010-05-06T20:18:55Z

KentWilliams at 20:17, 6 May 2010

2010-05-06T20:17:55Z

KentWilliams: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features NOTOC ===Module Name=== BRAINSROIAuto {| |[[Image:B…'

2010-05-06T20:16:52Z

Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== BRAINSROIAuto {| |[[Image:B…'

New page

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSROIAuto

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

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
*IO Parameters
**Input Image Volume: Image for which mask should be generated
**Output Mask: Output binary image volume, defining the mask.
**Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.
*Configuration Parameters
**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
**Otsu Threshold Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
**Closing Size: The size for the largest void to fill in the mask, in voxels.
**Output Image Pixel Type: the scalar type of the masked output volume.
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

== Development ==

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

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===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.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

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

@@ Line 81: / Line 81: @@
 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.
-<!== ===Source code & documentation===
+<!--
 Links to the module's source code:

@@ Line 56: / Line 56: @@
 *Configuration Parameters
 **Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
-**Otsu Threshold Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
+**Otsu Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
 **Closing Size: The size for the largest void to fill in the mask, in voxels.
 **Output Image Pixel Type: the scalar type of the masked output volume.

@@ Line 59: / Line 59: @@
 **Closing Size: The size for the largest void to fill in the mask, in voxels.
 **Output Image Pixel Type: the scalar type of the masked output volume.
-|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
+|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
 |}