Modules:Volumes:Diffusion Editor-Documentation-3.6 - Revision history

Grundlett: Text replacement - "https?:\/\/www.slicer.org\/slicerWiki\/index.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1"

2019-11-27T14:52:36Z

Text replacement - "https?:\/\/www.slicer.org\/slicerWiki\/index.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1"

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

2019-11-27T02:24:47Z

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

Kerstin at 19:08, 14 April 2010

2010-04-14T19:08:02Z

Kerstin at 18:55, 14 April 2010

2010-04-14T18:55:40Z

Kerstin at 18:45, 14 April 2010

2010-04-14T18:45:05Z

Kerstin at 18:38, 14 April 2010

2010-04-14T18:38:02Z

Kerstin at 18:30, 14 April 2010

2010-04-14T18:30:08Z

Kerstin at 18:19, 14 April 2010

2010-04-14T18:19:14Z

Kerstin at 18:09, 14 April 2010

2010-04-14T18:09:11Z

Kerstin: template

2010-04-14T17:50:47Z

template

New page

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

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

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

== 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 ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

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

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

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

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===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 120: / Line 120: @@
 The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.
 * The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [[Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module].|Changes there have an immediate impact for the tracts in the Diffusion Editor.
-* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module]].
+* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [https://www.slicer.org/wiki/Slicer3:DTMRI#Tractography_Module]].* See [[Slicer3:DTMRI#Tractography_Module|here]] for more information on the Tractography modules.
 ===Dependencies===

@@ Line 111: / Line 111: @@
 The Diffusion Editor uses the Tensor Estimation CLM (Command Line Module) of Slicer to compute tensors.
 * The module provides the linear-least-squares, non-linear-least squares and weighted-least-square method for the estimation. But the DiffusionEditor uses the linear-least-squares method by default, as it is the fastest and most robust.
-* See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tensor_Estimation_from_DWI_Module], [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:TeemExamples#tend_estim:_tensor_estimation] for more information on the Tensor Estimation CLM.
+* See [[Slicer3:DTMRI#Tensor_Estimation_from_DWI_Module],|[http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:TeemExamples#tend_estim:_tensor_estimation]] for more information on the Tensor Estimation CLM.
 The testing frame provides just a small subset of DTI display options. For more detailed settings
@@ Line 119: / Line 119: @@
 ==== Used Tractography Fiducial Seeding ====
 The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.
-* The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module]. Changes there have an immediate impact for the tracts in the Diffusion Editor.
+* The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [[Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module].|Changes there have an immediate impact for the tracts in the Diffusion Editor.
-* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module].
+* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module]].
-* See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module here] for more information on the Tractography modules.
+* See [[Slicer3:DTMRI#Tractography_Module|here]] for more information on the Tractography modules.
 ===Dependencies===
@@ Line 149: / Line 149: @@
 ** Future work: Adding different views of gradients/bValues.
 * Checking gradients when one types new values in the textbox is slowly. Reason: SetDiffusionGradients of the vtkMRMLDiffusionWeightedVolumeNode seems to trigger many events.
-** Future work: Use [http://www.slicer.org/slicerWiki/index.php/Slicer3:EventBroker Eventbroker] for performance analysis and if necessary turn off events.
+** Future work: Use [[Slicer3:EventBroker|Eventbroker]] for performance analysis and if necessary turn off events.
 ===Source code & documentation===
@@ Line 183: / Line 183: @@
 ===References===
-[http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf Thesis]
+[[Image:Thesis_letter.pdf|Thesis]]
-[http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI DTMRI]
+[[Slicer3:DTMRI|DTMRI]]
 [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format Nrrd format]
 [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI DICOM for DWI and DTI]

← Older revision		Revision as of 19:08, 14 April 2010
Line 126:		Line 126:

	No other modules or packages are required for this module's use.		No other modules or packages are required for this module's use.
		+
		+	===Tests===
		+
		+	On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:
		+
		+	*[http://svn.slicer.org/Slicer3/trunk/Modules/Volumes/Testing/DiffusionEditor_GradientsTest.tcl DiffusionEditor_GradientsTest.tcl]
		+	*[http://svn.slicer.org/Slicer3/trunk/Modules/Volumes/Testing/DiffusionEditorTensorTest.tcl DiffusionEditorTensorTest.tcl]
		+	*[http://svn.slicer.org/Slicer3/trunk/Modules/Volumes/Testing/DiffusionEditorTest.tcl DiffusionEditorTest.tcl]
		+	*[http://svn.slicer.org/Slicer3/trunk/Modules/Volumes/Testing/DiffusionEditor_GradientsTest.tcl DiffusionEditor_GradientsTest.tcl]

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

@@ Line 21: / Line 21: @@
 ===Authors, Collaborators & Contact===
-* Author1: Kerstin Kessel
+* Author: Kerstin Kessel
-* Contact: kerstin@bwh.harvard.edu
+* Contributor: Steve Pieper
 ===Module Description===

@@ Line 29: / Line 29: @@
 The Diffusion Editor is a 3D Slicer module, which allows modifying parameters (gradients, bValues, measurement frame) of DWI data and provides a quick way to interpret them. For that it estimates a tensor and shows glyphs and tracts for visual exploration.
 == Usage ==
@@ Line 124: / Line 122: @@
 * See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module here] for more information on the Tractography modules.
 ===Usability issues===
@@ Line 135: / Line 140: @@
 * Checking gradients when one types new values in the textbox is slowly. Reason: SetDiffusionGradients of the vtkMRMLDiffusionWeightedVolumeNode seems to trigger many events.
 ** Future work: Use [http://www.slicer.org/slicerWiki/index.php/Slicer3:EventBroker Eventbroker] for performance analysis and if necessary turn off events.
 ===Source code & documentation===

@@ Line 30: / Line 30: @@
 The Diffusion Editor is a 3D Slicer module, which allows modifying parameters (gradients, bValues, measurement frame) of DWI data and provides a quick way to interpret them. For that it estimates a tensor and shows glyphs and tracts for visual exploration.
 == Usage ==
@@ Line 122: / Line 105: @@
 ===Notes from the Developer(s)===
-Algorithms used, library classes depended upon, use cases, etc.
+==== Measurement Frame ====
-===Dependencies===
+==== Used Tensor Estimation ====
-Other modules or packages that are required for this module's use.
+The testing frame provides just a small subset of DTI display options. For more detailed settings
-===Tests===
+==== Used Tractography Fiducial Seeding ====
+The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.
-On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:
+* The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module]. Changes there have an immediate impact for the tracts in the Diffusion Editor.
+* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module].
-* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
+* See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module here] for more information on the Tractography modules.
@@ Line 153: / Line 142: @@
 Source code:
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.cxx
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.cxx vtkSlicerDiffusionEditorWidget.cxx]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.h
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.h vtkSlicerDiffusionEditorWidget.h]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.cxx
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.cxx vtkSlicerDiffusionEditorLogic.cxx]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.h
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.h vtkSlicerDiffusionEditorLogic.h]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.cxx
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.cxx vtkSlicerMeasurementFrameWidget.cxx]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.h
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.h vtkSlicerMeasurementFrameWidget.h]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.cxx
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.cxx vtkSlicerGradientsWidget.cxx]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.h
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.h vtkSlicerGradientsWidget.h]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.cxx
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.cxx vtkSlicerDiffusionTestingWidget.cxx]
-*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.h
+*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.h vtkSlicerDiffusionTestingWidget.h]
 Doxygen documentation:
-*http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerDiffusionEditorWidget.html
+*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerDiffusionEditorWidget.html SlicerDiffusionEditorWidget]
-*http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerDiffusionEditorLogic.html
+*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerDiffusionEditorLogic.html DiffusionEditorLogic]
-*http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerGradientsWidget.html
+*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerGradientsWidget.html GradientsWidget]
-*http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerDiffusionTestingWidget.html
+*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerDiffusionTestingWidget.html DiffusionTestingWidget]
 == More Information ==

@@ Line 62: / Line 62: @@
 * Use Case 2: Edit the measurement frame as described above.
 * Use Case 3: Test the parameters by displaying glyphs and tracts.
 ===Tutorials===
@@ Line 89: / Line 87: @@
 ===Quick Tour of Features and Use===
 {|
@@ Line 140: / Line 135: @@
 * MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]
-Links to known bugs in the Slicer3 bug tracker
+===Usability issues===
-===Usability issues===
+* Changing the measurement frame of a DTI has no impact. The tensor is not estimated again.
 ===Source code & documentation===
@@ Line 156: / Line 153: @@
 Source code:
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
+*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.cxx
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]
+*http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.h
 Doxygen documentation:
-*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
+*http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerDiffusionEditorWidget.html
 == More Information ==
 ===Acknowledgment===
-Include funding and other support here.
+This research project was part of a Master thesis (Diplomarbeit) in cooperation of the faculty of Medical Informatics, University of Heidelberg/Germany and the Surgical Planning Lab. It was supported by a grant of the Lions Club Heilbronn/Franken.
 ===References===
-Publications related to this module go here. Links to pdfs would be useful.
+[http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf Thesis]

@@ Line 25: / Line 25: @@
 ===Module Description===
-Overview of what the module does goes here.
 == Usage ==
@@ Line 39: / Line 61: @@
 For DTI
 * Use Case 2: Edit the measurement frame as described above.
-* Use Case 3: Test by displaying glyphs and tracts.
+* Use Case 3: Test the parameters by displaying glyphs and tracts.
-[[Image:DiffusionEditor_v8.jpg|right|overview]]
+===Quick Tour of Features and Use===
 * '''Measurement frame:'''
 # The determinant of the measurement frame has to be 1. This is checked by the editor.
@@ Line 71: / Line 120: @@
 ## Tract visibility: Add some fiducials and choose the fiducial list in the selector. Show tracts with Tractography Fiducial Seeding.
+|[[Image:DiffusionEditor_v8.jpg|thumb|280px|User Interface]]
 |}

@@ Line 4: / Line 4: @@
 __NOTOC__
-===Module Name===
+===Module Name ===
-MyModule
+Diffusion Editor
 {|
-|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
+|[[Image:DiffusionEditor helix.jpg         |thumb|250px|Diffusion Editor, showing tracts and glyphs on helix example]]
-|[[Image:screenshotBlank.png|thumb|280px|Output]]
+|[[Image:Tracts_glyphs.jpg                     |thumb|250px|tracts and glyphs view]]
-|[[Image:screenshotBlank.png|thumb|280px|Caption]]
+|[[Image:Tracts_glyphs_90degrees.jpg |thumb|250px|tracts and glyphs view - +90° rotation of measurement frame]]
 |}
@@ Line 16: / Line 16: @@
 ===Module Type & Category===
-Type: Interactive or CLI
+Type: Interactive
-Category: Base or (Filtering, Registration, ''etc.'')
+Category: Diffusion Imaging
 ===Authors, Collaborators & Contact===
-* Author1: Affiliation & logo, if desired
+* Author1: Kerstin Kessel
-* Contributor1: Affiliation & logo, if desired
+* Contact: kerstin@bwh.harvard.edu
 ===Module Description===
@@ Line 35: / Line 33: @@
 This module is especially appropriate for these use cases:
-* Use Case 1:
+For DWI
-* Use Case 2:
+* Use Case 1: Edit gradients manually or load existing gradients from file (.txt or .nhdr).
 Examples of the module in use:
-* Example 1
+* '''Measurement frame:'''
-* Example 2
+# The determinant of the measurement frame has to be 1. This is checked by the editor.
 ===Tutorials===