Modules:ChangeTracker-Documentation-3.6 - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/images\/([^ ]+) ([^]]+)]" to "[http://www.slicer.org/w/img_auth.php/$1 $2]"

2019-11-27T12:39:22Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/images\/([^ ]+) ([^]]+)]" to "[http://www.slicer.org/w/img_auth.php/$1 $2]"

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:33:12Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Grundlett: Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:14:52Z

Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Fedorov at 03:45, 22 November 2011

2011-11-22T03:45:14Z

Fedorov at 13:23, 10 June 2010

2010-06-10T13:23:09Z

Fedorov: /* Tests */

2010-04-24T22:36:24Z

Tests

Fedorov: /* Tests */

2010-04-24T22:35:03Z

Tests

Fedorov: /* Tests */

2010-04-24T22:34:36Z

Tests

Fedorov: /* Usability issues */

2010-04-16T03:15:50Z

Usability issues

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

2010-04-16T03:13:58Z

Quick Tour of Features and Use

@@ Line 45: / Line 45: @@
 ===Tutorials===
-[http://www.slicer.org/slicerWiki/images/4/4d/Slicer3.4.1-ChangeTrackerTutorial.pdf Tutorial slides]
+[http://www.slicer.org/w/img_auth.php/4/4d/Slicer3.4.1-ChangeTrackerTutorial.pdf Tutorial slides]
 {|
 |The supplemental data for the tutorial can be loaded automatically (you need to have access to the Internet to do this). Go to the "Help and Acknowledgment" tab, and hit "Load tutorial data" button.

@@ Line 59: / Line 59: @@
 |Use drop-down controls to choose the two scans where you would like to measure pathology development. Currently, we support analysis of the images that correspond to two time points. Extending of the module to accept more than two time points is the feature under development.
-Note, that ChangeTracker does not "see" transforms located above volume nodes in the MRML hierarchy. If you want any transform in the MRML tree to be used as the initial pose of the image, you will need to create a new volume by resampling the original volume. Slicer3 module [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 ResampleVolume2] can be used for this purpose.
+Note, that ChangeTracker does not "see" transforms located above volume nodes in the MRML hierarchy. If you want any transform in the MRML tree to be used as the initial pose of the image, you will need to create a new volume by resampling the original volume. Slicer3 module [[Modules:ResampleVolume2-Documentation-3.4|ResampleVolume2]] can be used for this purpose.
 |[[Image:ChangeTracker_Step1.png|thumb|250px|Step 1: Scan selection]]

@@ Line 148: / Line 148: @@
 ===Dependencies===
-ChangeTracker depends on the following modules: [http://wiki.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes], [http://wiki.slicer.org/slicerWiki/index.php/Modules:RigidRegistration-Documentation-3.6 Rigid Registration], [http://wiki.slicer.org/slicerWiki/index.php?title=Modules:DiffeomorphicDemonsAlgorithm-Documentation03.4&action=edit DiffeomorphicDemons]
+ChangeTracker depends on the following modules: [[Modules:Volumes-Documentation-3.6|Volumes]], [[Modules:RigidRegistration-Documentation-3.6|Rigid Registration]], [http://wiki.slicer.org/slicerWiki/index.php?title=Modules:DiffeomorphicDemonsAlgorithm-Documentation03.4&action=edit DiffeomorphicDemons]
 {|
+|
-[http://wiki.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes] module is required for the general tasks of new volume creation etc. This module should always be available in your Slicer, but can be turned off in the Slicer Application Settings. Make sure it is available.
+[[Modules:Volumes-Documentation-3.6|Volumes]] module is required for the general tasks of new volume creation etc. This module should always be available in your Slicer, but can be turned off in the Slicer Application Settings. Make sure it is available.
 ChangeTracker is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation-3.6 Rigid Registration module] through the CommandLineModule shared object invocation. Note, that there are two distinct rigid registration modules in Slicer, which have identical functionality: "Linear registration" and "Rigid registration". Both of these modules should be available in your build, but "Rigid registration" *must* be available for ChangeTracker to function properly. You can verify the availability of the module manually by looking at the list of modules in the registration category.

@@ Line 66: / Line 66: @@
 * '''Step 2: Define volume of interest'''
-This step of wizard includes the following user cotrols to facilitate Volume of Interest (VOI) selection:
+This step of wizard includes the following user controls to facilitate Volume of Interest (VOI) selection:
 * "Hide/show render" button: used to control visibility of volume rendering for the selected region
 * "Reset" button: reset the selected region to start over

← Older revision		Revision as of 13:23, 10 June 2010
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	[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]		[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]
−
−	~~'''This documentation page is under development'''~~

	__NOTOC__		__NOTOC__

@@ Line 163: / Line 163: @@
 The following tests verify some of the functionality of the module on the [http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer dashboard].
-[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/vtkChangeTrackerGUITest.cxx vtkChangeTrackerGUITest.cxx]
+[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/vtkChangeTrackerGUITest.cxx vtkChangeTrackerGUITest.cxx]: exercise basic functionality of the GUI classes
-[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/vtkMRMLChangeTrackerNodeTest.cxx vtkMRMLChangeTrackerNodeTest.cxx]
+[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/vtkMRMLChangeTrackerNodeTest.cxx vtkMRMLChangeTrackerNodeTest.cxx]: exercise basic functionality of the MRML node
-[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/CMakeLists.txt ChangeTrackerCL_Help]
+[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/CMakeLists.txt ChangeTrackerCL_Help]: verify correct execution of the command line module without any action
-[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/CMakeLists.txt ChangeTrackerCL_TestFull_Intensity]
+[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/CMakeLists.txt ChangeTrackerCL_TestFull_Intensity]: command line module to exercise some of the functionality in ChangeTracker logic
 ===Known bugs===

← Older revision		Revision as of 22:34, 24 April 2010
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	[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/vtkMRMLChangeTrackerNodeTest.cxx vtkMRMLChangeTrackerNodeTest.cxx]		[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/vtkMRMLChangeTrackerNodeTest.cxx vtkMRMLChangeTrackerNodeTest.cxx]
		+
		+	[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ChangeTracker/Testing/CMakeLists.txt ChangeTrackerCL_Help and ChangeTrackerCL_TestFull_Intensity]

	===Known bugs===		===Known bugs===

@@ Line 178: / Line 178: @@
 |ChangeTracker is using rigid registration module to automatically align the input images and selected volumes of interest. It is possible, that rigid registration can fail to align your data. If this happens, you will see error message in the pop-up box, as shown to the right.
-You can try to solve this problem by manually registering your data prior to using it with ChangeTracker. You can try to register your data by using the [http://www.slicer.org/slicerWiki/index.php?title=Modules:Rigid-registration-Documentation-3.4 Rigid registration module] and manually adjusting the registration parameters to have satisfactory result of registration. Note, that you will need to select "Create new volume" while running registration, and use that volume together with the fixed image as inputs to ChangeTracker.
+You can try to solve this problem by manually registering your data prior to using it with ChangeTracker, placing Scan2 under the transform in the MRML hierarchy, and choosing "I have a transform that aligns my data" in the '''Advanced''' tab of Step 4.
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker to report any usability issues. Please select the '''usability issue category''' when browsing or contributing.

@@ Line 105: / Line 105: @@
 {|
 |We provide two metrics to quantify tumor progression: intensity-based and deformation-based (see details in this [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430 paper]). Choose the metric(s) you would like to use.
-|[[Image:ChangeTracker_Step4.png|thumb|250px|Step 4: Metric selection]]
 |}