Modules:TransformFromFiducials-Documentation-3.6 - Revision history

Gcasey: moved Modules:FiducialRegistration-Documentation-3.6 to Modules:TransformFromFiducials-Documentation-3.6

2010-03-28T17:50:32Z

moved Modules:FiducialRegistration-Documentation-3.6 to Modules:TransformFromFiducials-Documentation-3.6

Gcasey at 17:27, 28 March 2010

2010-03-28T17:27:09Z

Gcasey: moved Modules:FiducialRegistration-Documentation-3.5 to Modules:FiducialRegistration-Documentation-3.6

2010-03-28T17:25:47Z

moved Modules:FiducialRegistration-Documentation-3.5 to Modules:FiducialRegistration-Documentation-3.6

Gcasey: /* Source code & documentation */

2010-02-05T14:46:54Z

Source code & documentation

Gcasey at 14:46, 5 February 2010

2010-02-05T14:46:02Z

Gcasey at 14:45, 5 February 2010

2010-02-05T14:45:37Z

Gcasey at 14:44, 5 February 2010

2010-02-05T14:44:51Z

Gcasey: /* References */

2010-02-05T14:33:06Z

References

Gcasey: First draft of transform from fiducials documentation

2010-02-05T14:32:52Z

First draft of transform from fiducials documentation

Gcasey: Start transform from fiducials documentation by copying template

2010-02-05T14:18:30Z

Start transform from fiducials documentation by copying template

New page

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

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

Type: Interactive or CLI

Category: Base or (Filtering, Registration, ''etc.'')

===Authors, Collaborators & Contact===
* Author1: Affiliation & logo, if desired
* Contributor1: Affiliation & logo, if desired
* Contributor2: Affiliation & logo, if desired
* Contact: name, email

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===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===

Customize following links for your module:

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 1: / Line 1: @@
-[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
+[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
-[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]
+[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
 ===Transform From Fiducials===

@@ Line 60: / Line 60: @@
 Source code:
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/RegisterImagesModule/Applications TransformFromFidcuals.cxx ]
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/RegisterImagesModule/Applications/TransformFromFiducials.cxx TransformFromFidcuals.cxx ]
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/RegisterImagesModule/Applications/TransformFromFiducials.xml TransformFromFidcuals.xml ]
 ===Acknowledgment===

@@ Line 8: / Line 8: @@
 {|
-|[[Image:FiducialRegistration_Before.jpg|thumb|280px|Images with fiducials attached by user]]
+|[[Image:Fiducial_registration_before.jpg|thumb|280px|Images with fiducials attached by user]]
-|[[Image:FiducialRegistration_After.jpg|thumb|280px|Images with transform applied to moving image based on fiducial alignment]]
+|[[Image:Fiducial_registration_after.jpg|thumb|280px|Images with transform applied to moving image based on fiducial alignment]]
 |}

@@ Line 8: / Line 8: @@
 {|
-|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
+|[[Image:FiducialRegistration_Before.jpg|thumb|280px|Images with fiducials attached by user]]
+|[[Image:FiducialRegistration_After.jpg|thumb|280px|Images with transform applied to moving image based on fiducial alignment]]
 |}

@@ Line 68: / Line 68: @@
 ===References===
-Berthold K. P. Horn (1987),
+ Berthold K. P. Horn (1987),
-"Closed-form solution of absolute orientation using unit quaternions,"
+ "Closed-form solution of absolute orientation using unit quaternions,"
   Journal of the Optical Society of America A, 4:629-642

← Older revision	Revision as of 17:50, 28 March 2010
(No difference)

← Older revision	Revision as of 17:25, 28 March 2010
(No difference)

@@ Line 9: / Line 9: @@
 {|
 |[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
-|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
 |}
@@ Line 16: / Line 15: @@
 ===Module Type & Category===
-Type: Interactive or CLI
+Type: CLI
-Category: Base or (Filtering, Registration, ''etc.'')
+Category: Registration
 ===Authors, Collaborators & Contact===
-* Author1: Affiliation & logo, if desired
+* Author1: Casey Goodlett, Kitware
-* Contributor1: Affiliation & logo, if desired
+* Contributor1: Dominik Meier, BWH
-* Contributor2: Affiliation & logo, if desired
+* Contact: Casey Goodlett
 ===Module Description===
-Overview of what the module does goes here.
+This module computs a linear transform from two lists of fiducials.  The transform can either be translation only, rigid transform, or similarity transform.
 == Usage ==
 ===Examples, Use Cases & Tutorials===
-* Note use cases for which this module is especially appropriate, and/or link to examples.
+* Use case 1: Registration initialization.  If the user can specify a few anatomical points (at least 3), this module can be used to generate a transform which can be used to initialize image based registration.
-* Link to examples of the module's use
+* IGT tasks that generate landmarks from a tracker automatically can use this module to compute transforms.
 ===Quick Tour of Features and Use===
-* '''Input panel:'''
+* '''Main panel:'''
-* '''Parameters panel:'''
+** Fixed landmarks - target list of points.  The resulting transform maps an object onto the fixed landmarks.
-* '''Output panel:'''
+** Moving landmarks - source list of points.  The result transform maps objects from this space to the fixed landmark space.
-* '''Viewing panel:'''
+** Save Transform - Transform node to save the result in.  Typically a new transform should be created.
 == Development ==
+This module is based on [http://www.itk.org/Doxygen/html/classitk_1_1LandmarkBasedTransformInitializer.html itk::LandmarkBasedTransformInitializer].  Additional code is internally used in the module to compute the scaling factor for similarity transforms.  This code is based on (Horn 1987).
 ===Known bugs===
@@ Line 61: / Line 59: @@
 ===Source code & documentation===
 Source code:
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/RegisterImagesModule/Applications TransformFromFidcuals.cxx ]
 ===Acknowledgment===
-Include funding and other support here.
+This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from National Centers for Biomedical Computing.
 ===References===
-Publications related to this module go here. Links to pdfs would be useful.
+Berthold K. P. Horn (1987),