Modules:MaskImage-Documentation-3.6 - Revision history

Harveerar: /* Use Cases, Examples */

2010-04-27T13:12:29Z

Use Cases, Examples

Harveerar: /* Use Cases, Examples */

2010-04-27T13:12:16Z

Use Cases, Examples

Harveerar: /* Use Cases, Examples */

2010-04-26T14:40:23Z

Use Cases, Examples

Harveerar: /* Use Cases, Examples */

2010-04-26T14:31:31Z

Use Cases, Examples

Nicole: /* Quick Tour of Features and Use */

2010-04-13T15:45:37Z

Quick Tour of Features and Use

Nicole: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features NOTOC ===Mask Image=== Mask Image {| |[[Image:MaskI…'

2010-04-13T15:44:32Z

Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Mask Image=== Mask Image {| |[[Image:MaskI…'

New page

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

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

__NOTOC__
===Mask Image===
Mask Image

{|
|[[Image:MaskImage_Module_icon.png|thumb|280px|Mask Image GUI]]
|[[Image:MaskImageModule_snapshot_1.png|thumb|280px|Mask Image Input: Image + Labelmap]]
|[[Image:MaskImageModule_snapshot_2.png|thumb|280px|Mask Image Output]]
|}

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

Type: CLI

Category: Filtering, Arithmetic

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

===Module Description===

Apply a labelmap as a mask and set all pixels outside the mask (i.e. not matching the label value) to zero (or a given replacement value)

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: masking unwanted structures in processes that do not support masking directly.

Examples of the module in use:

* Example 1:

===Tutorials===

Links to tutorials explaining how to use this module:


===Quick Tour of Features and Use===
*'''Input Volume:''' the image to be masked
*'''Mask Volume:''' labelmap containing the region to be preserved as a specific (single) label value
*'''Masked Volume:''' result image created. Equals the Input Volume with all voxels not part of the mask replaced.
*'''Label Value:''' value of the Mask Volume to use as ROI. All voxels '''not''' matching this value will be replaced. All voxels matching this value will be preserved.
*'''Replace Value:''' value to set for all voxels "outside" the mask. To remove unwanted structure, zero (0) is the common default. All voxels not matching the Label Value above will be set to this Replace Value.

== Development ==

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

This is a wrapper around the itk::ThresholdImageFilter.

===Dependencies===

The Volumes module is 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:

* MaskTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Testing/MaskTest.cxx Applications/CLI/Testing/MaskTest.cxx]

===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===

* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Mask.cxx?view=log Mask.cxx]
* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Mask.xml?view=log Mask.xml]



== More Information ==

===Acknowledgment===

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

===References===

@@ Line 39: / Line 39: @@
 * Example Test: Shows an example of recovering the bone structures using a mask on the CT images
-*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/Testing/MaskTest.cxx MaskTest.cxx]
+[http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/Testing/MaskTest.cxx MaskTest.cxx]
 ===Tutorials===

@@ Line 34: / Line 34: @@
 This module is especially appropriate for these use cases:
-* Use Case 1: Removing unwanted structures or keeping structures that are of interest for inspection or further processing.
+* Use Case 1: Removing unwanted structures.
 Examples of the module in use:

@@ Line 49: / Line 49: @@
 ===Quick Tour of Features and Use===
-*'''Input Volume:''' the image to be masked
+*'''Input and Output:'''
-*'''Mask Volume:''' labelmap containing the region to be preserved as a specific (single) label value
+**'''Input Volume:''' the image to be masked
-*'''Masked Volume:''' result image created. Equals the Input Volume with all voxels not part of the mask replaced.
+**'''Mask Volume:''' labelmap containing the region to be preserved as a specific (single) label value
-*'''Label Value:'''  value of the Mask Volume to use as ROI. All voxels '''not''' matching this value will be replaced. All voxels matching this value will be preserved.
+**'''Masked Volume:''' result image created. Equals the Input Volume with all voxels not part of the mask replaced.
-*'''Replace Value:''' value to set for all voxels "outside" the mask. To remove unwanted structure, zero (0) is the common default. All voxels not matching the Label Value above will be set to this Replace Value.
+*'''Settings:'''
 == Development ==

Modules:MaskImage-Documentation-3.6 - Revision history

Harveerar: /* Use Cases, Examples */

Harveerar: /* Use Cases, Examples */

Harveerar: /* Use Cases, Examples */

Harveerar: /* Use Cases, Examples */

Nicole: /* Quick Tour of Features and Use */

Nicole: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Mask Image=== Mask Image {| |[[Image:MaskI…'

Nicole: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features NOTOC ===Mask Image=== Mask Image {| |[[Image:MaskI…'