Documentation/4.0/Modules/TractographyDisplay - Revision history

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:30:14Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

JChris.FillionR at 10:37, 2 February 2012

2012-02-02T10:37:27Z

Marianna at 18:38, 29 November 2011

2011-11-29T18:38:50Z

Demian at 23:19, 25 November 2011

2011-11-25T23:19:52Z

Demian at 23:16, 25 November 2011

2011-11-25T23:16:47Z

Demian at 23:11, 25 November 2011

2011-11-25T23:11:38Z

Demian at 21:05, 25 November 2011

2011-11-25T21:05:08Z

Marianna: Created page with ' {{documentation/{{documentation/version}}/module-header}} {{doc…'

2011-11-11T21:18:45Z

Created page with ' {{documentation/{{documentation/version}}/module-header}}   {{doc…'

New page

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Demian Wassermann, SPL 
Contributor1: FIRSTNAME LASTNAME, AFFILIATION 
Contributor2: FIRSTNAME LASTNAME, AFFILIATION 
Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.




If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre>

If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>

Using this later template, the final syntax would be:
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>





{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1:
* Use Case 2:


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

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

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}




{{note}}The section above is generated using the following wiki code:
<pre>
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}
</pre>

If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre>

If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre>

Using this later template, the final syntax would be:
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre>





{{documentation/{{documentation/version}}/module-footer|category=Example}}

← Older revision		Revision as of 07:30, 14 June 2013
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	{{documentation/{{documentation/version}}/module-header}}		{{documentation/{{documentation/version}}/module-header}}

@@ Line 10: / Line 10: @@
 Author: Isaiah Norton, Goldby Lab<br>
 Author: Demian Wassermann, SPL<br>
-Contributor1: Steve Pieper, Isomics<br>
+Contributor1: Steve Pieper, Isomics Inc.<br>
-Contributor1: Alex Yarmanovich, Isomics<br>
+Contributor2: Alex YarmarKovich, Isomics Inc.<br>
 Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
 {{documentation/{{documentation/version}}/module-introduction-row}}
@@ Line 35: / Line 35: @@
 * Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
 * Use Case 2: Display the tracts as lines or tubes
-* Use Case 2: Interactive selection or cropping of a certain bundle.
+* Use Case 3: Interactive selection or cropping of a certain bundle.
 <!-- ---------------------------- -->
@@ Line 48: / Line 48: @@
 {|style="width: 100%"
+|
-* Input panel1:
-** First input
+** Line: Display the tracts as lines
-** Second input
+** Tube: Display the tracts as tubes
-* Parameters panel:
+*** Slice Intersection: Show the tracts in the 2D view
-** First parameter
+** Glyph: Display glyphs representing the diffusion tensors along the tracts
 ** Second parameter
 * Output panel:
@@ Line 75: / Line 79: @@
 [[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
 |}
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@@ Line 88: / Line 88: @@
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
 {{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}
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 {{documentation/{{documentation/version}}/module-footer|category=Example}}
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@@ Line 8: / Line 8: @@
 {{documentation/{{documentation/version}}/module-introduction-row}}
 This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
 Author: Demian Wassermann, SPL<br>
-Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br>
+Contributor1: Steve Pieper, Isomics<br>
-Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br>
+Contributor1: Alex Yarmanovich, Isomics<br>
 Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
 {{documentation/{{documentation/version}}/module-introduction-row}}

@@ Line 44: / Line 44: @@
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}
-A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:
+[[image:2011-11-12-CroppingWholeBrainTractography.png|400px]]
 {|style="width: 100%"

@@ Line 56: / Line 56: @@
 * Fiber Bundle Selection: Perform interactive selection and cropping of the tracts
 ** ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts
-** Disable/Positive/Negative ROI: Set the selection mode to '''select everything'''; '''select the tracts traversing the ROI'''; '''Select the tracts not traversing the ROI'''
+** Disable/Positive/Negative ROI: Set the selection mode to '''Select everything'''; '''Select the tracts traversing the ROI'''; '''Select the tracts not traversing the ROI'''
-** Second parameter
+** Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones
-* Output panel:
+** Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
-** First output
+* Advance Display: For the lines, tubes and glyphs
-** Second output
+** Visibility: Toggle the visibility of the bundle
-* Viewing panel:
+** Opacity: Change the transparency level of the bundle
 | align="right" |
 [[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
 | align="right" |
 [[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
 |}
 <!-- ---------------------------- -->

@@ Line 22: / Line 22: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
+Allows the user to manipulate several different characteristics of the traced white matter tracts. Examples are: change of color; display of the fractional anisotropy along the tract; display of the tracts as tubes or lines; interactive selection of the tracts; and cropping.
 <!-- ----------------------------------------------------------------- -->
 <!-- ----------------------------------------------------------------- -->
@@ Line 43: / Line 33: @@
 Most frequently used for these scenarios:
-* Use Case 1:
+* Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
-* Use Case 2:
+* Use Case 2: Display the tracts as lines or tubes
 <!-- ---------------------------- -->