Slicer3:Model Into Label Volume Documentation-3.4 - Revision history

Nicole: /* Examples, Use Cases & Tutorials */

2009-10-14T14:31:57Z

Examples, Use Cases & Tutorials

Marianna at 20:18, 26 May 2009

2009-05-26T20:18:56Z

Nicole: /* Examples, Use Cases & Tutorials */

2009-04-06T21:52:34Z

Examples, Use Cases & Tutorials

Nicole: /* Examples, Use Cases & Tutorials */

2009-04-06T21:51:49Z

Examples, Use Cases & Tutorials

Nicole: /* Examples, Use Cases & Tutorials */

2009-04-06T21:40:30Z

Examples, Use Cases & Tutorials

Nicole: /* Source code & documentation */

2009-02-13T17:06:59Z

Source code & documentation

Nicole at 19:29, 12 February 2009

2009-02-12T19:29:57Z

Nicole: /* Usage */

2009-02-12T17:11:17Z

Usage

Nicole: New page: Return to Slicer 3.4 Documentation NOTOC ===Model Into Label Volume=== ModelIntoLabelVolume {| |[[Image:ModelIntoLabelVolumeGUI.jpg|thumb|280px|Screenshot of th...

2009-02-12T17:09:56Z

New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Model Into Label Volume=== ModelIntoLabelVolume {| |[[Image:ModelIntoLabelVolumeGUI.jpg|thumb|280px|Screenshot of th...

New page

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Model Into Label Volume===
ModelIntoLabelVolume

{|
|[[Image:ModelIntoLabelVolumeGUI.jpg|thumb|280px|Screenshot of the GUI]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive, scripted in Tcl.

Category: Model Generation

===Authors, Collaborators & Contact===
* Nicole Aucoin: Brigham and Women's Hospital
* Contact: Nicole Aucoin, nicole@bwh.harvard.edu

===Module Description===
Intersect a model with a reference volume and create an output label map volume with the model vertices labeled with the given label value.

== Usage ==

Select a model node and a reference volume node from the MRML Scene.
Optionally, you can select a label value that will be inserted into the new label volume, as well as a name for the new label volume. If you don't select a label value, 2 will be used. If you leave the Label Volume Name field blank, a new name will be created from the name of the model and the name of the reference volume.
If you choose to set the use intensity flag, the voxel values in the reference volume will be copied to the output label map. This will result in a colorful label map until you reset the color node associated with the new label volume, but is useful for calculating statistics at the model intersection with the reference volume.
If you choose to set the subdivide model flag, before the intersection is done, the model will be subdivided so that it contains more vertices from which to calculate the intersection with the reference volume. Useful with sparse reference volumes.
The default labels color look up table will be assigned to the new label map volume.

===Examples, Use Cases & Tutorials===

* This module is especially useful once fibre tracts have been generated for a DTI case. Intersect the tract model with the FA reference volume.


===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Settings panel:''' this module has a single panel, see the Usage section above for details.

== Development ==

===Dependencies===

The Models and Volumes modules 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.

===Source code & documentation===

Customize following
[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ModelIntoLabelVolume/ Source Code].

As this is a module scripted in TCL, there is no C++ doxygen documentation.

== More Information ==

===Acknowledgment===

Work on this module was funded through NA-MIC.

===References===

@@ Line 41: / Line 41: @@
 |[[Image:SlicerModelIntoLabelMapBackToModel-3.4.jpg|thumb|280px|Regenerating a model from the generated label map, using the opacity slider to show the fibre tracts inside.]]
 |}
 ===Quick Tour of Features and Use===

@@ Line 36: / Line 36: @@
 {|
 |[[Image:SlicerModelIntoLabelMapBefore-3.4.jpg|thumb|280px|Setting up, using seeded fibre tracts from a fiducial, using the helix mask as a reference volume.]]
-|[[Image:SlicerModelIntoLabelMapAfter-3.4.jpg|thumb|280px|After running, overlaying the new label volume on the helix DTI volume]]
+|[[Image:SlicerModelIntoLabelMapAfter-3.4.jpg|thumb|280px|After running, overlaying the new label volume on the helix DTI volume. This shows a solid label map as the fibre tracts are grouped close to each other.]]
 |[[Image:SlicerModelIntoLabelMapBackToModel-3.4.jpg|thumb|280px|Regenerating a model from the generated label map, using the opacity slider to show the fibre tracts inside.]]
 |}

@@ Line 34: / Line 34: @@
 -->
-[[Image:SlicerModelIntoLabelMapBefore-3.4.jpg|thumb|280px|Setting up]]
+{|
+|[[Image:SlicerModelIntoLabelMapBefore-3.4.jpg|thumb|280px|Setting up, using seeded fibre tracts from a fiducial, using the helix mask as a reference volume.]]
-[[Image:SlicerModelIntoLabelMapAfter-3.4.jpg|thumb|280px|After running]]
+|[[Image:SlicerModelIntoLabelMapAfter-3.4.jpg|thumb|280px|After running, overlaying the new label volume on the helix DTI volume]]
+|[[Image:SlicerModelIntoLabelMapBackToModel-3.4.jpg|thumb|280px|Regenerating a model from the generated label map, using the opacity slider to show the fibre tracts inside.]]
-[[Image:SlicerModelIntoLabelMapBackToModel-3.4.jpg|thumb|280px|Regenerating a model from the generated label map, using the opacity slider to show the fibre tracts inside.]]
+|}
 ===Quick Tour of Features and Use===

@@ Line 1: / Line 1: @@
 [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Model Into Label Volume===
@@ Line 17: / Line 19: @@
 ===Authors, Collaborators & Contact===
 * Nicole Aucoin: Brigham and Women's Hospital
-* Contact: Nicole Aucoin, nicole@bwh.harvard.edu
+* Contact: Nicole Aucoin, nicole at bwh.harvard.edu
 ===Module Description===

@@ Line 33: / Line 33: @@
 * Link to any existing tutorials
 -->
 ===Quick Tour of Features and Use===

@@ Line 62: / Line 62: @@
 ===Source code & documentation===
-−
 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ModelIntoLabelVolume/ Source Code].
 As this is a module scripted in TCL, there is no C++ doxygen documentation.
 == More Information ==

@@ Line 24: / Line 24: @@
 == Usage ==
-Select a model node and a reference volume node from the MRML Scene.
+Select a model node and a reference volume node from the MRML Scene, press the Apply Button.
 ===Examples, Use Cases & Tutorials===
@@ Line 45: / Line 37: @@
 List all the panels in your interface, their features, what they mean, and how to use them. For instance:
-* '''Settings panel:''' this module has a single panel, see the Usage section above for details.
+* '''Settings panel:''' this module has a single panel, all options are controlled here.
 == Development ==
 ===Dependencies===
@@ Line 56: / Line 56: @@
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.
 ===Usability issues===

Slicer3:Model Into Label Volume Documentation-3.4 - Revision history

Nicole: /* Examples, Use Cases & Tutorials */

Marianna at 20:18, 26 May 2009

Nicole: /* Examples, Use Cases & Tutorials */

Nicole: /* Examples, Use Cases & Tutorials */

Nicole: /* Examples, Use Cases & Tutorials */

Nicole: /* Source code & documentation */

Nicole at 19:29, 12 February 2009

Nicole: /* Usage */

Nicole: New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Model Into Label Volume=== ModelIntoLabelVolume {| |[[Image:ModelIntoLabelVolumeGUI.jpg|thumb|280px|Screenshot of th...

Nicole: New page: Return to Slicer 3.4 Documentation NOTOC ===Model Into Label Volume=== ModelIntoLabelVolume {| |[[Image:ModelIntoLabelVolumeGUI.jpg|thumb|280px|Screenshot of th...