Modules:DTIDisplay-Documentation-3.4 - Revision history

Nicole: /* Usability issues */

2010-01-15T22:14:59Z

Usability issues

Marianna at 19:34, 26 May 2009

2009-05-26T19:34:24Z

Alexy: /* Display */

2009-04-05T16:19:47Z

Display

Alexy: /* Module Name */

2009-04-05T16:17:44Z

Module Name

Alexy: /* Usability issues */

2009-03-03T19:07:58Z

Usability issues

Alexy at 22:22, 16 February 2009

2009-02-16T22:22:16Z

Alexy: New page: Return to Slicer 3.4 Documentation NOTOC ===Module Name=== '''DisplayLoadSave''' Module Panel == General Informati...

2009-02-16T21:08:09Z

New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Module Name=== '''DisplayLoadSave''' thumb|350px|Right|Module Panel == General Informati...

New page

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
'''DisplayLoadSave'''

[[Image:Models-Module.png|thumb|350px|Right|Module Panel]]

== General Information ==
===Module Type & Category===
Type: Interactive

Category: Tractography

===Authors, Collaborators & Contact===
* Alex Yarmarkovich, Isomics, SPL
* Contact: Alex Yarmarkovich, alexy@bwh.harvard.edu

===Module Description===
This module is used for loading, saving, changing the appearance of, and organizing 3d surface models.
== Usage ==
=Load=
*Load Model allows the user to load a single model, of any type that Slicer recognizes. This includes VTK polydata, BYU, XML polydata, STL files and FreeSurfer surface files.
*Load Model directory will load all the VTK models (*.vtk) that are located in in the selected directory
*Load FreeSurfer Overlay will load a FreeSurfer scalar overlay file and associate it with the currently active model. The active model must be a FreeSurfer surface model (e.g. from files named *.pial, *.orig, etc)

=Display=
*Model Select: Select the model that you want to modify from a list
*Visibility: Turn a model on or off in the 3D window
*Scalar visibility: If the model has a scalar field you can make it visible or not using this check box.
*Set Active Scalar: Select from the list of currently loaded scalar overlays. Most models will have normals, Freesurfer surface models can have multiple scalar overlay files associated with them (e.g. lh.sulc, lh.curv).
* Scalar Color Map Select: select the color mapping used to map from the scalar overlay's values (usually in the range of 0.0 to 1.0) to colors. There are built in color maps that can be browsed in the Colors module. The most commonly used color map for FreeSurfer scalar overlays is the GreenRed one. Legacy color maps from Slicer2 include Grey, Iron, Rainbow, etc. Those color maps with "labels" in their names are usually discrete and don't work well for the continuous scalar overlay ranges.
*Clipping: Set clipping on or off for this model. Once it is on, go to the Clipping pane to set the options.
*Backface Culling: Set back face culling on or off for this model.
*Opacity: Set how transparent this model is
*Set Color: Set the base color for this model. Only visible if the Scalar Visibility is off.
*Material Properties: This collection of options allows you to change the appearance of the model.
**Some presets can be selected at the bottom of this pane. A preview sphere lets you adjust the values with immediate feedback.
**Ambient: controls the base lighting for the model
**Diffuse: controls the amount of light scattered from the model
**Specular: controls the highlights on the model
**Power: sets the specular power

=Save=

*Model To Save: select a model from the list.
*Save Model: opens a file browser to let you select the location to which to save the file. The valid extensions and file types that can be used are:
**.vtk poly data
**.vtp xml poly data
**.stl STL

=Model Display=
* Allows to adjust the visualization properties of individual models or model hierarchies.
* Color, Scalar fields, opacity and material properties can be set.
* Clipping enables clipping for that particular structure
* Backface culling is turned on by default. This means that all the faces pointing away from the view point of the camera, are not rendered. This feature needs to be turned off if the inside of a model is viewed, either when clipping or when moving the camera inside an object.

=Save Model=
*Is used to save a model.
* '''It is important to remember to provide the extension''', typically .vtk (e.g. MyModel.vtk)

===Examples, Use Cases & Tutorials===
* Tutorial about [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training
loading and viewing data].

===Quick Tour of Features and Use===
* '''Load:''' Load models into Slicer3
* '''Display:''' Adjust modles display parameters
* '''Save:''' Saves models onto disk

== 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.

Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Tractography/Display/ link] to the ChangeTracker source code in ViewVC.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classes.html Documentation] generated by doxygen.

== More Information ==

===Acknowledgment===

===References===

@@ Line 77: / Line 77: @@
 Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Tractography/Display/ link] to the source code in ViewVC.
-[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classes.html Documentation] generated by doxygen.
+[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html Documentation] generated by doxygen.
 == More Information ==

@@ Line 33: / Line 33: @@
 * Visibility: Turn a fiber bundle on or off in the 3D window
 * Color By Scalar: Select from the list of derived tensor scalar properties such as Fractional Anisotropy, etc.
-* Scalar Color Map:Sselect the color mapping used to map from the scalar values to colors.
+* Scalar Color Map: Select the color mapping used to map from the scalar values to colors.
 * Clipping: Set clipping on or off for this bundle. Once it is on, go to the Models->Clipping pane to set the options.
 * Opacity: Set how transparent this track is.

@@ Line 1: / Line 1: @@
 [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Module Name===

@@ Line 2: / Line 2: @@
 __NOTOC__
 ===Module Name===
-'''DisplayLoadSave'''
+'''FiberBundles'''
 {|

@@ Line 72: / Line 72: @@
 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.
-Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Tractography/Display/ link] to the ChangeTracker source code in ViewVC.
+Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Tractography/Display/ link] to the source code in ViewVC.
 [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classes.html Documentation] generated by doxygen.

@@ Line 4: / Line 4: @@
 '''DisplayLoadSave'''
-[[Image:Models-Module.png|thumb|350px|Right|Module Panel]]
+{|
 == General Information ==
@@ Line 17: / Line 21: @@
 ===Module Description===
-This module is used for loading, saving, changing the appearance of, and organizing 3d surface models.
+This module is used for loading, saving, and changing the appearance of DTI fiber tracts.
 == Usage ==
 =Load=
-*Load Model allows the user to load a single model, of any type that Slicer recognizes. This includes VTK polydata, BYU, XML polydata, STL files and FreeSurfer surface files.
+* Load Tractography allows the user to load a single track file. The file should be a VTK polydata file (.vtk or .vtp) containing polylines with Tensor point data.
-*Load Model directory will load all the VTK models (*.vtk) that are located in in the selected directory
+*Load Tractography directory will load all the VTK models (*.vtk) that are located in in the selected directory
 =Display=
-*Model Select: Select the model that you want to modify from a list
+* Fiber Bundle Select: Select the bundle that you want to modify from a list
-*Visibility: Turn a model on or off in the 3D window
+* Display for Lines/Tubes/Glyphs: select which representation to edit. Note that you can have more than one representation visible at the same time, for example Lines and Glyphs.
-*Scalar visibility: If the model has a scalar field you can make it visible or not using this check box.
+* Visibility: Turn a fiber bundle on or off in the 3D window
-*Set Active Scalar: Select from the list of currently loaded scalar overlays. Most models will have normals, Freesurfer surface models can have multiple scalar overlay files associated with them (e.g. lh.sulc, lh.curv).
+* Color By Scalar: Select from the list of derived tensor scalar properties such as Fractional Anisotropy, etc.
-* Scalar Color Map Select: select the color mapping used to map from the scalar overlay's values (usually in the range of 0.0 to 1.0) to colors. There are built in color maps that can be browsed in the Colors module. The most commonly used color map for FreeSurfer scalar overlays is the GreenRed one. Legacy color maps from Slicer2 include Grey, Iron, Rainbow, etc. Those color maps with "labels" in their names are usually discrete and don't work well for the continuous scalar overlay ranges.
+* Scalar Color Map:Sselect the color mapping used to map from the scalar values to colors.
-*Clipping: Set clipping on or off for this model. Once it is on, go to the Clipping pane to set the options.
+* Clipping: Set clipping on or off for this bundle. Once it is on, go to the Models->Clipping pane to set the options.
-*Backface Culling: Set back face culling on or off for this model.
+* Opacity: Set how transparent this track is.
-*Opacity: Set how transparent this model is
+* Set Color: Set the base color for this bundle.
-*Set Color: Set the base color for this model. Only visible if the Scalar Visibility is off.
+* Glyph Display Properties: Only applicable to glyphs.
-*Material Properties: This collection of options allows you to change the appearance of the model.
+** Glyph Type: Lines, Tubes, or Ellipsoids.
-**Some presets can be selected at the bottom of this pane. A preview sphere lets you adjust the values with immediate feedback.
+** Scale factor: Controls glyph size.
-**Ambient: controls the base lighting for the model
+** Spacing: Controls the number of glyphs along the tract.
 =Save=
+*Fiber Bundle To Save: Select a bundle from the list.
-*Model To Save: select a model from the list.
+*Save Tractography: Opens a file browser to let you select the location to which to save the file. The valid extensions and file types that can be used are:
 **.vtk poly data
 **.vtp xml poly data
 ===Examples, Use Cases & Tutorials===
@@ Line 65: / Line 54: @@
 ===Quick Tour of Features and Use===
-* '''Load:''' Load models into Slicer3
+* '''Load:''' Load fiber tracts into Slicer3
-* '''Display:''' Adjust modles display parameters
+* '''Display:''' Adjust track display parameters
 * '''Save:''' Saves models onto disk