Documentation/Nightly/Modules/TractographyDisplay - Revision history

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

2019-11-27T13:15:13Z

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

Zhangfanmark at 20:26, 6 July 2016

2016-07-06T20:26:10Z

Lauren at 16:35, 6 July 2016

2016-07-06T16:35:40Z

Lauren at 16:29, 6 July 2016

2016-07-06T16:29:29Z

Lauren at 16:26, 6 July 2016

2016-07-06T16:26:58Z

Lauren at 16:25, 6 July 2016

2016-07-06T16:25:12Z

Zhangfanmark at 21:10, 29 June 2016

2016-06-29T21:10:54Z

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

2013-06-14T08:03:18Z

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

JChris.FillionR: 4.1 -> Nightly

2012-08-22T17:05:31Z

4.1 -> Nightly

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: Isaiah Norton, Goldby Lab 
Author: Demian Wassermann, SPL 
Contributor1: Steve Pieper, Isomics Inc. 
Contributor2: Alex YarmarKovich, Isomics Inc. 
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}}
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.


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

* 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 3: Interactive selection or cropping of a certain bundle.


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


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

[[image:2011-11-12-CroppingWholeBrainTractography.png|400px]]

{|style="width: 100%"
|
*
** Line: Display the tracts as lines
** Tube: Display the tracts as tubes
*** Slice Intersection: Show the tracts in the 2D view
** Glyph: Display glyphs representing the diffusion tensors along the tracts
** Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
* 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'''
** Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones
** Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
* Advance Display: For the lines, tubes and glyphs
** Visibility: Toggle the visibility of the bundle
** Opacity: Change the transparency level of the bundle
** Color By: Change the way the bundle is colored; either by a tensor-derived property or by a group id
** Solid Color: Color the bundle of a single solid color



{{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}}


{{documentation/{{documentation/version}}/module-footer}}

@@ Line 8: / Line 8: @@
 {{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].<br>
-Author: Isaiah Norton, Goldby Lab<br>
+Title: Tractography Display
-Author: Demian Wassermann, SPL<br>
-Contributor1: Steve Pieper, Isomics Inc.<br>
+Author(s)/Contributor(s): Demian Wassermann, Isaiah Norton, Lauren O'Donnell, Steve Pieper, Alex Yarmarkovich (SPL, LMI, BWH, SlicerDMRI)
-Contributor2: Alex YarmarKovich, Isomics Inc.<br>
-Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
+License: 3D Slicer Contribution and Software License Agreement
 {{documentation/{{documentation/version}}/module-introduction-row}}
 {{documentation/{{documentation/version}}/module-introduction-logo-gallery
@@ Line 27: / Line 34: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-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.
+Allows the user to modify the display of diffusion tractography. 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.
 <!-- ---------------------------- -->

← Older revision		Revision as of 08:03, 14 June 2013
Line 1:		Line 1:
		+	<noinclude>{{documentation/versioncheck}}</noinclude>
	<!-- ---------------------------- -->		<!-- ---------------------------- -->
	{{documentation/{{documentation/version}}/module-header}}		{{documentation/{{documentation/version}}/module-header}}

@@ Line 47: / Line 47: @@
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
 Links to tutorials that use this module
-* Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial
+* Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}

@@ Line 57: / Line 57: @@
+|
 * Simple Display
-** Line: Display the tracts as lines
+** Solid Tube Color: Display the tracts as tubes in solid color, if checked
-** Tube: Display the tracts as tubes
+** Lines: Display the tracts as lines
-*** Slice Intersection: Show the tracts in the 2D view (Tubes Slice)
+** Tubes: Display the tracts as tubes
-** Glyph: Display glyphs representing the diffusion tensors along the tracts
+** Tubes Slice: Show the tracts in the 2D view (Tubes Slice)
 ** Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
-* Fiber Bundle Selection: Perform interactive selection and cropping of the tracts
+* Fiber Bundle Selection: Perform 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'' or ''Select the tracts not traversing the ROI''
-** Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones
+** Interactive ROI: Allow the fiber selection and cropping in an interactive way
 ** Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
 * Advanced Display: For the lines, tubes and glyphs
 ** Visibility: Toggle the visibility of the bundle
 ** Opacity: Change the transparency level of the bundle
-** Color By: Change the way the bundle is colored; either by a tensor-derived property or by a group id
+** Fiber Bundle Coloring: Change the way the bundle is colored, one of "Of Tensor Property", "Of Scalar Value", "Color Fibers By Mean Orientation", "Color Fibers By Segment Orientation", "Of Fiber Cluster Group ID" or "Solid Color".
-** Solid Color: Color the bundle of a single solid color
+*** Auto W/L: Adjust the window level automatically
 <!--
 | align="right" |

@@ Line 67: / Line 67: @@
 ** Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones
 ** Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
-* Advance Display: For the lines, tubes and glyphs
+* Advanced Display: For the lines, tubes and glyphs
 ** Visibility: Toggle the visibility of the bundle
 ** Opacity: Change the transparency level of the bundle
@@ Line 79: / Line 79: @@
 |}
 -->
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
-Publications related to this module go here. Links to pdfs would be useful.
+*  http://slicerdmri.github.io/
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
-{{documentation/{{documentation/version}}/module-developerinfo}}
+* https://github.com/SlicerDMRI
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-footer}}
 <!-- ---------------------------- -->