https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=HarveerarSlicer Wiki - User contributions [en]2026-04-17T08:14:32ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23420Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-28T12:43:47Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result: Multiplier=2.5, Neighborhood radius=1, Number of Iterations=5]]<br />
|}<br />
This module is useful for obtaining a 2-class segmentation. The fiducials are placed on parts of the image that correspond to the target (foreground). The segmentation can be refined by modifying the number of iterations, the multiplier, and the neighborhood radius options available on the user interface panel. Additionally, the user may also place additional fiducials on the image.<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The user interface panel:<br />
{|<br />
|[[Image:simpleregiongrowingUI.png|280px|User interface panel]]<br />
|}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* [[Documentation/4.0/Modules/Robust Statistics Segmentation|Robust Statistics Segmentation]]<br />
* GrowCut segmentation in the editor module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<!-- Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
--><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- {{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
--><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23419Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-28T12:42:52Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result: Multiplier=2.5, Neighborhood=1, Iterations=5]]<br />
|}<br />
This module is useful for obtaining a 2-class segmentation. The fiducials are placed on parts of the image that correspond to the target (foreground). The segmentation can be refined by modifying the number of iterations, the multiplier, and the neighborhood radius options available on the user interface panel. Additionally, the user may also place additional fiducials on the image.<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The user interface panel:<br />
{|<br />
|[[Image:simpleregiongrowingUI.png|280px|User interface panel]]<br />
|}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* [[Documentation/4.0/Modules/Robust Statistics Segmentation|Robust Statistics Segmentation]]<br />
* GrowCut segmentation in the editor module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<!-- Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
--><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- {{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
--><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0&diff=23275Documentation/4.02011-11-25T14:40:46Z<p>Harveerar: /* Segmentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!-- TODO: Create a template that will list all documentation links --><br />
<small><span class="versionlist">[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]</span></small><br />
<br />
=Table of Content=<br />
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"<br />
|-<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
|- <br />
|valign="top"|<br />
<br />
===Slicer Application===<br />
----<br />
<big>'''<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)<br />
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. --><br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)''' <br />
</big><br />
<br />
===Mailing Lists===<br />
----<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]<br />
<br />
<!--<br />
*[[Modules:ExtensionsManagementWizard-Documentation-4.0| Extensions Management Wizard]] (xx)<br />
--><br />
<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Module Categories ===<br />
----<br />
<big>'''<br />
* [[#Core Modules|Core Modules]]<br />
* [[#Wizards|Wizards]]<br />
* [[#Informatics|Informatics]]<br />
* [[#Registration|Registration]]<br />
* [[#Segmentation|Segmentation]]<br />
* [[#Quantification|Quantification]]<br />
* [[#Diffusion|Diffusion]]<br />
* [[#IGT|IGT]]<br />
* [[#Filtering|Filtering]]<br />
* [[#Surface Models|Surface Models]]<br />
* [[#Converters|Converters]]<br />
* [[#Endoscopy|Endoscopy]]<br />
* [[#Developer Tools|Developer Tools]]<br />
* [[#Legacy|Legacy]]<br />
* [[#Utilities|Utility]]<br />
</big><br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Miscellaneous===<br />
----<br />
<!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --><br />
<br />
* [[Slicer4:VisualBlog|Visual blog]]<br />
: Set of screenshots showing Slicer in action.<br />
<br />
<!--<br />
* [[Documents and links]]<br />
: Set of presentations made on Slicer and document talking about it.<br />
<br />
--><br />
* [[Documentation/4.0/Training|Training pages]]<br />
: Information on how to use Slicer {{documentation/version}}<br />
<br />
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br />
: Set of common questions/answers<br />
<br />
===Developers Corner===<br />
----<br />
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]<br />
: Handy Developer Info<br />
|}<br />
<br />
=General Information=<br />
{|width="100%"<br />
|rowspan="3"|<br />
{{Infobox<br />
|name = 3D Slicer {{documentation/version}}<br />
|above = 3D Slicer<br />
|abovestyle = <br />
<br />
|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]<br />
|imagestyle = <br />
|headerstyle = background:#E7DCC3;<br />
|labelstyle = <br />
|datastyle = <br />
<br />
|header1 = Description<br />
|label1 = <br />
|data1 =<br />
|header2 =<br />
|label2 = <br />
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.<br />
|header3 =<br />
|label3 = <br />
|data3 = Free and extensible open source package.<br />
|header4 =<br />
|label4 = Multi-platform<br />
|data4 = Linux, MacOSX, Windows<br />
|header5 =<br />
|label5 = Version<br />
|data5 = {{documentation/version}}<br />
|header6 =<br />
|label6 = License<br />
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]<br />
}}<br />
|align="center"|<br />
[[{{collaborator|logo|slicer4}}|x350px]] <br />
|-<br />
|<br />
{{ombox<br />
|type=content<br />
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].<br />
}}<br />
|-<br />
|<br />
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}<br />
|}<br />
<br />
=Requirements for Modules=<br />
* The module is '''feature complete''', i.e. it does everything that it advertises<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.<br />
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].<br />
* Use logos listed in the [[Template:Collaborator|Collaborators Template]].<br />
<br />
=Modules by Category=<br />
==Core Modules==<br />
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br />
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Wizards==<br />
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
<br />
==Informatics==<br />
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br />
<br />
==Registration==<br />
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*Specialized<br />
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**Vector Demon Registration (Hans Johnson)<br />
<br />
==Segmentation==<br />
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
*Specialized<br />
**EMSegment Command-line (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)<br />
<br />
==Quantification==<br />
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)<br />
* Change quantification<br />
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br />
<br />
==Diffusion== <br />
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Tractography<br />
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Utilities<br />
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==IGT==<br />
<br />
==Filtering==<br />
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Resample Tools<br />
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Arithmetic <br />
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br />
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Morphology<br />
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)<br />
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Surface Models==<br />
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Label Map Smoothing<br />
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Converters==<br />
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br />
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Endoscopy==<br />
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br />
<br />
==Developer Tools==<br />
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<br />
*Module Template<br />
*Multiple Models Example<br />
*Performance Tests<br />
*Tractography<br />
<br />
==Legacy==<br />
*Converters<br />
**BSpline to Deformation Field<br />
*Diffusion<br />
**Denoising<br />
***Unbiased Non Local Means Filter for DWI<br />
*Filtering<br />
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
**Resample Scalar Volume<br />
*Registration<br />
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Nonrigid BSpline Registration<br />
**Expert Automated Registration<br />
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Robust Multiresolution Affine Registration<br />
*Segmentation<br />
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Utilities==<br />
*Transform MRML Files to NewSegmenter Standard<br />
<br />
=Extensions=<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.<br />
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.<br />
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.<br />
<br />
==Collections==<br />
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyCollection<br />
| This is a collection of extensions that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
==Table Of Extensions==<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something wonderful with your data<br />
| [[File:ExperimentalExtensionIcon.png|80px]]<br />
| [[File:NoSlicerLicenseIcon.png|80px]]<br />
| filter, anisotropic<br />
| my-email at gmail.com<br />
|-<br />
| 2<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
'''Caption for the table of extensions'''<br />
<gallery heights="50px" perrow="4"><br />
Image:SlicerLicenseIcon.png| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]<br />
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License<br />
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess)<br>Use with care<br>Might not work all the time<br>Might not be available for all platforms<br />
Image:StableExtensionIcon.png|Stable <br>Full documentation <br>Works as advertised <br>Compiles on all supported platforms<br>Email support works<br />
</gallery></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0&diff=23273Documentation/4.02011-11-25T14:40:03Z<p>Harveerar: </p>
<hr />
<div>__NOTOC__<br />
<br />
<!-- TODO: Create a template that will list all documentation links --><br />
<small><span class="versionlist">[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]</span></small><br />
<br />
=Table of Content=<br />
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"<br />
|-<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
|- <br />
|valign="top"|<br />
<br />
===Slicer Application===<br />
----<br />
<big>'''<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)<br />
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. --><br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)''' <br />
</big><br />
<br />
===Mailing Lists===<br />
----<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]<br />
<br />
<!--<br />
*[[Modules:ExtensionsManagementWizard-Documentation-4.0| Extensions Management Wizard]] (xx)<br />
--><br />
<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Module Categories ===<br />
----<br />
<big>'''<br />
* [[#Core Modules|Core Modules]]<br />
* [[#Wizards|Wizards]]<br />
* [[#Informatics|Informatics]]<br />
* [[#Registration|Registration]]<br />
* [[#Segmentation|Segmentation]]<br />
* [[#Quantification|Quantification]]<br />
* [[#Diffusion|Diffusion]]<br />
* [[#IGT|IGT]]<br />
* [[#Filtering|Filtering]]<br />
* [[#Surface Models|Surface Models]]<br />
* [[#Converters|Converters]]<br />
* [[#Endoscopy|Endoscopy]]<br />
* [[#Developer Tools|Developer Tools]]<br />
* [[#Legacy|Legacy]]<br />
* [[#Utilities|Utility]]<br />
</big><br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Miscellaneous===<br />
----<br />
<!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --><br />
<br />
* [[Slicer4:VisualBlog|Visual blog]]<br />
: Set of screenshots showing Slicer in action.<br />
<br />
<!--<br />
* [[Documents and links]]<br />
: Set of presentations made on Slicer and document talking about it.<br />
<br />
--><br />
* [[Documentation/4.0/Training|Training pages]]<br />
: Information on how to use Slicer {{documentation/version}}<br />
<br />
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br />
: Set of common questions/answers<br />
<br />
===Developers Corner===<br />
----<br />
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]<br />
: Handy Developer Info<br />
|}<br />
<br />
=General Information=<br />
{|width="100%"<br />
|rowspan="3"|<br />
{{Infobox<br />
|name = 3D Slicer {{documentation/version}}<br />
|above = 3D Slicer<br />
|abovestyle = <br />
<br />
|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]<br />
|imagestyle = <br />
|headerstyle = background:#E7DCC3;<br />
|labelstyle = <br />
|datastyle = <br />
<br />
|header1 = Description<br />
|label1 = <br />
|data1 =<br />
|header2 =<br />
|label2 = <br />
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.<br />
|header3 =<br />
|label3 = <br />
|data3 = Free and extensible open source package.<br />
|header4 =<br />
|label4 = Multi-platform<br />
|data4 = Linux, MacOSX, Windows<br />
|header5 =<br />
|label5 = Version<br />
|data5 = {{documentation/version}}<br />
|header6 =<br />
|label6 = License<br />
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]<br />
}}<br />
|align="center"|<br />
[[{{collaborator|logo|slicer4}}|x350px]] <br />
|-<br />
|<br />
{{ombox<br />
|type=content<br />
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].<br />
}}<br />
|-<br />
|<br />
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}<br />
|}<br />
<br />
=Requirements for Modules=<br />
* The module is '''feature complete''', i.e. it does everything that it advertises<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.<br />
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].<br />
* Use logos listed in the [[Template:Collaborator|Collaborators Template]].<br />
<br />
=Modules by Category=<br />
==Core Modules==<br />
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br />
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Wizards==<br />
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
<br />
==Informatics==<br />
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br />
<br />
==Registration==<br />
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*Specialized<br />
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**Vector Demon Registration (Hans Johnson)<br />
<br />
==Segmentation==<br />
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller) <br />
*Specialized<br />
**EMSegment Command-line (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)<br />
<br />
==Quantification==<br />
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)<br />
* Change quantification<br />
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br />
<br />
==Diffusion== <br />
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Tractography<br />
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Utilities<br />
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==IGT==<br />
<br />
==Filtering==<br />
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Resample Tools<br />
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Arithmetic <br />
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br />
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Morphology<br />
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)<br />
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Surface Models==<br />
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Label Map Smoothing<br />
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Converters==<br />
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br />
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Endoscopy==<br />
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br />
<br />
==Developer Tools==<br />
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<br />
*Module Template<br />
*Multiple Models Example<br />
*Performance Tests<br />
*Tractography<br />
<br />
==Legacy==<br />
*Converters<br />
**BSpline to Deformation Field<br />
*Diffusion<br />
**Denoising<br />
***Unbiased Non Local Means Filter for DWI<br />
*Filtering<br />
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
**Resample Scalar Volume<br />
*Registration<br />
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Nonrigid BSpline Registration<br />
**Expert Automated Registration<br />
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Robust Multiresolution Affine Registration<br />
*Segmentation<br />
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Utilities==<br />
*Transform MRML Files to NewSegmenter Standard<br />
<br />
=Extensions=<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.<br />
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.<br />
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.<br />
<br />
==Collections==<br />
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyCollection<br />
| This is a collection of extensions that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
==Table Of Extensions==<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something wonderful with your data<br />
| [[File:ExperimentalExtensionIcon.png|80px]]<br />
| [[File:NoSlicerLicenseIcon.png|80px]]<br />
| filter, anisotropic<br />
| my-email at gmail.com<br />
|-<br />
| 2<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
'''Caption for the table of extensions'''<br />
<gallery heights="50px" perrow="4"><br />
Image:SlicerLicenseIcon.png| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]<br />
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License<br />
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess)<br>Use with care<br>Might not work all the time<br>Might not be available for all platforms<br />
Image:StableExtensionIcon.png|Stable <br>Full documentation <br>Works as advertised <br>Compiles on all supported platforms<br>Email support works<br />
</gallery></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23272Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T14:38:37Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result]]<br />
|}<br />
This module is useful for obtaining a 2-class segmentation. The fiducials are placed on parts of the image that correspond to the target (foreground). The segmentation can be refined by modifying the number of iterations, the multiplier, and the neighborhood radius options available on the user interface panel. Additionally, the user may also place additional fiducials on the image.<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The user interface panel:<br />
{|<br />
|[[Image:simpleregiongrowingUI.png|280px|User interface panel]]<br />
|}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* [[Documentation/4.0/Modules/Robust Statistics Segmentation|Robust Statistics Segmentation]]<br />
* GrowCut segmentation in the editor module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<!-- Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
--><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- {{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
--><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23269Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T14:36:01Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result]]<br />
|}<br />
This module is useful for obtaining a 2-class segmentation. The fiducials are placed on parts of the image that correspond to the target (foreground). The segmentation can be refined by modifying the number of iterations, the multiplier, and the neighborhood radius options available on the user interface panel. Additionally, the user may also place additional fiducials on the image.<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The user interface panel:<br />
{|<br />
|[[Image:simpleregiongrowingUI.png|280px|User interface panel]]<br />
|}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* [[Documentation/4.0/Modules/Robust Statistics Segmentation|Robust Statistics Segmentation]]<br />
* GrowCut segmentation in the editor module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23266Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T14:06:39Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result]]<br />
|}<br />
This module is useful for obtaining a 2-class segmentation. The fiducials are placed on parts of the image that correspond to the target (foreground). The segmentation can be refined by modifying the number of iterations, the multiplier, and the neighborhood radius options available on the user interface panel. Additionally, the user may also place additional fiducials on the image.<br />
<br />
<!-- ---------------------------- --><br />
<!-- {{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The user interface panel:<br />
{|<br />
|[[Image:simpleregiongrowingUI.png|280px|User interface panel]]<br />
|}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23265Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T14:04:55Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result]]<br />
|}<br />
This module is useful for obtaining a 2-class segmentation. The fiducials are placed on parts of the image that correspond to the target (foreground). The segmentation can be refined by modifying the number of iterations, the multiplier, and the neighborhood radius options available on the user interface panel. Additionally, the user may also place additional fiducials on the image.<br />
<br />
<!-- ---------------------------- --><br />
>!-- {{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The user interface panel:<br />
{|<br />
|[[Image:simpleregiongrowingUI|280px|User interface panel]]<br />
|}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23264Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T14:02:10Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result]]<br />
|}<br />
This module is useful for obtaining a 2-class segmentation. The fiducials are placed on parts of the image that correspond to the target (foreground). The segmentation can be refined by modifying the number of iterations, the multiplier, and the neighborhood radius options available on the user interface panel. Additionally, the user may also place additional fiducials on the image.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23263Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T13:56:52Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|400px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|450px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|450px|Segmentation result]]<br />
|}<br />
<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23262Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T13:56:19Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|300px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|350px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|350px|Segmentation result]]<br />
|}<br />
<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23261Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T13:55:37Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{|<br />
|[[Image:slicerToolbar1.png|thumb|280px|Fiducial tool bar icon]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|280px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|280px|Segmentation result]]<br />
|}<br />
<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:SlicerToolbar1.png&diff=23260File:SlicerToolbar1.png2011-11-25T13:54:53Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23259Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T13:54:30Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
The fiducial tool bar icon (identified inside a red box) on the Slicer tool bar is shown.<br />
{[[Image:slicerToolbar1.png|thumb|280px|Fiducial tool bar icon]]}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowing.png|thumb|280px|User input in the form of fiducials]]<br />
|[[Image:ressimpleregion.png|thumb|280px|Segmentation result]]<br />
|}<br />
<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:Ressimpleregion.png&diff=23258File:Ressimpleregion.png2011-11-25T13:29:20Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:Simpleregiongrowing.png&diff=23257File:Simpleregiongrowing.png2011-11-25T13:28:46Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:SimpleregiongrowingUI.png&diff=23256File:SimpleregiongrowingUI.png2011-11-25T13:28:06Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/SimpleRegionGrowingSegmentation&diff=23255Documentation/4.0/Modules/SimpleRegionGrowingSegmentation2011-11-25T13:27:38Z<p>Harveerar: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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><br />
Author: Jim Miller, GE<br><br />
Contact: Jim Miller <email>millerjv@ge.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:NAMIC 380x463.jpg|NA-MIC<br />
|Image:GE-logo.png|GE <br />
|Image:Itk-logo.jpg|Itk<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
This module can be used to obtain a volumetric segmentation of a region of interest.<br />
Most frequently used for these scenarios:<br />
<br />
* Example volumetric segmentation of a tumor given a set of fiducial points selected on the tumor:<br />
{|<br />
|[[Image:simpleregiongrowingUI.png|thumb|280px|Caption 1]]<br />
|[[Image:simpleregiongrowing.png|thumb|280px|Caption 2]]<br />
|[[Image:ressimpleregion.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml?p=17347 }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
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><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
{{documentation/{{documentation/version}}/module-category|xmlurl=http://svn.slicer.org/Slicer4/trunk/Applications/CLI/ConfidenceConnected/ConfidenceConnected.xml }}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Harveerarhttps://www.slicer.org/w/index.php?title=Slicer3:3.6_Final_Issues&diff=19094Slicer3:3.6 Final Issues2011-02-11T14:58:44Z<p>Harveerar: /* DONE: Issues fixed for inclusion in Slicer 3.6.3 */</p>
<hr />
<div>'''Notes: <br />
* Include the [http://www.na-mic.org/Bug/ mantis] bug number in your svn commit messages<br />
* Test your fixes in the slicer3 trunk - when you are sure they work, (1) move them to the Slicer-3-6 branch (2) move them from the TODO to the DONE category on this page<br />
* The Slicer3 repository is in maintenance mode - please do not add new features. New modules should be added only as [http://www.slicer.org/slicerWiki/index.php/Slicer3:Extensions extensions].<br />
'''<br />
<br />
==TODO: Issues to fix for the 3.6.4 patch release==<br />
<br />
<br />
* Integrate SPECTRE plugin as an extension once MIPAV is open sourced (Nicole)<br />
* Resample widget does not work properly in linked mode. In that situation, the slices should maintain the relative positions as the widget reorients them. (Steve, Jim, Michal)<br />
* Adjust the appearance of slices in 3D view [http://www.na-mic.org/Bug/view.php?id=1061 1061] Steve)<br />
* Interface settings in Application settings are not saved http://na-mic.org/Mantis/view.php?id=1076 (Steve?)<br />
<br />
==TODO: Issues to fix for the 3.6.3 patch release==<br />
''Fixes for these issues should be checked in to the Slicer-3-6 release branch by 3pm Eastern time on Monday, Feb 14, 2011''<br />
<br />
* Slice view toggles [http://www.na-mic.org/Bug/view.php?id=1003 1003] (Nicole)<br />
<br />
<br />
* BRAINSResample is not available as a shared library (C++ symbol name in .so) [http://www.na-mic.org/Bug/view.php?id=941 941] (Jim)<br />
* CompareView slice spacing issue [http://na-mic.org/Mantis/view.php?id=936 936] (Jim) <br />
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995] (Jim)<br />
* Compareviewer and crosshairs in Navigator mode: 4 compare viewers in wide screen mode (e.g. use [http://www.na-mic.org/Wiki/index.php/File:RSNA2010_fMRICase040Dataset.zip case 40] for data). text is not suppressed, display is slow. (Jim)<br />
* Migrate latest version of GrowCut into release branch (Harini and Jim)<br />
<br />
<br />
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.3 (Steve)<br />
* Create distribution binaries and extensions (Steve)<br />
<br />
<br />
<br />
** Move vtkEMSegmentLogic::AddDataIOFromScene to base code and replace in Slicer3.cxx corresponding code with function call<br />
** commandlines currently cannot execute links to files with http address <br />
* Data loading and FetchMI (Wendy -- fixes will be checked into trunk, and then migrated into branch... will update when complete):<br />
** http://na-mic.org/Mantis/view.php?id=1028 Request to compute checksum or md5sum and save as part of any storable node has registered as a feature request in Mantis. Plan right now is to create a method on MRMLScene->DataIOManager that will check for any data transfer with a status vtkDataTransfer::Failed. This status is set inside Base/Logic/vtkDataIOManagerLogic before data is loaded into slicer. Debugging this now...<br />
<br />
<br />
* Generate Robust MRI brain registration for EMSegmenter (Kilian, Dominik) <br />
* Include Atlas Creator (Kilian, Daniel)<br />
* Migrate EMSegment test fixes to the Slicer-3-6 release branch (Dominique, Kilian, Daniel)<br />
<br />
<br />
* Migrate BRAINS test fixes to the Slicer-3-6 release branch (Hans, Mark)<br />
<br />
<br />
=== DONE: Issues fixed for inclusion in Slicer 3.6.3 ===<br />
* File extension saving issues [http://na-mic.org/Mantis/view.php?id=1056 1056] [http://na-mic.org/Mantis/view.php?id=1064 1064] (Alex)<br />
* Warning and block when file type is changed using filename field in the Save dialog [http://www.na-mic.org/Bug/view.php?id=1064 1064] (Alex)<br />
* Display a warning message during installation on Windows if VC redistributable package is not installed (fix committed to the trunk by partyd on October 29, 2010)<br />
* Model Hierarchy issues [http://www.na-mic.org/Bug/view.php?id=961 961] (Alex)<br />
* Warning on unsaved data on scene close and exit (Alex)<br />
* Status of fade slider is not captured by scenesnapshot (Alexy).<br />
* Models Display UI cleanup (Alex)<br />
* models under transforms do not move after save/load scene [http://www.na-mic.org/Bug/view.php?id=1058 1058] (Alex)<br />
* multiple fiber tubes rendering performance (Alex)<br />
* Slicer crash related to fiducials/MRML [http://www.na-mic.org/Bug/view.php?id=1042 1042] (Alex)<br />
* Fixes to Camera/View handling (Alex & Wendy)<br />
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [[http://na-mic.org/Mantis/view.php?id=1036 1036], etc. (Alex)<br />
* Modify ProstateNav so that it does not get recompiled all the time. Fixed in rev [http://viewvc.slicer.org/viewcvs.cgi?rev=15446&sortby=rev&sortdir=down&view=rev 15446], now only one file is recompiled. (Andras)<br />
* Fixed BSplineDeformableRegistration (Fast non-rigid registration) CLI module to work correctly with rotated images (with direction cosines different from identity matrix) (Andras)<br />
* Fix for vtkITKBSpline transform save with scene snapshot [http://www.na-mic.org/Bug/view.php?id=1050] (Steve)<br />
* Fix for passing parameters to command line modules from Luca<br />
* Fix to CropVolume module to correctly propagate the name for the output volume (Andrey)<br />
* FastMarching crashes when applied two two different volumes one after another [http://www.na-mic.org/Bug/view.php?id=1057 1057] (Andrey)<br />
* ChangeTracker deformable metric did not work because demons binary was not properly installed (Andrey)<br />
* Setup node selector in LabelStatistics to allow label maps only (Andrey)<br />
* CropVolume would not work anymore after scene is closed (Andrey)<br />
* While in the volume rendering module, the render speed is slow while looking at a composited cross section. [http://www.na-mic.org/Bug/view.php?id=1052 1052]<br />
* http://na-mic.org/Mantis/view.php?id=983 (fixed)<br />
* Migrate DicomToNrrd fixes to the Slicer-3-6 release branch (Xiaodong)<br />
* Migrate MRML Node test fixes to the Slicer-3-6 release branch (Nicole)<br />
* Fix cygwin compile issue http://www.na-mic.org/Bug/view.php?id=1078 (Andras)<br />
* Model Maker naming bug [http://www.na-mic.org/Bug/view.php?id=1043 1043] (Nicole)<br />
* Loading *.mask files via 'Add Data' doesn't work [http://na-mic.org/Mantis/view.php?id=1067 1067] (Vince, Hans, Dominique)<br />
* Expose step size parameter for Endoscopy (Steve)<br />
* Label Grid should be off by default and should not come on automatically (Steve)<br />
* Slice volume selectors are reset after executing CLI http://na-mic.org/Mantis/view.php?id=1077 (Steve)<br />
* 4D Image: origin is not consistent with "Add volume" loaded data [http://www.na-mic.org/Bug/view.php?id=1000 1000] (Steve, Andrey, Junichi, Isaiah)<br />
* Switch to tclkit for running genlib to work around [http://viewvc.slicer.org/viewcvs.cgi?rev=15824&view=rev cygwin tclsh PATH] issue (Steve and Andras)<br />
* fix 3 view layout with endoscopy, external, and volume rendering view in distinct viewers to support Jay's programmaticly defined use-case (Steve) (not all functionality will be exposed in the GUI).<br />
** switching layouts loses observers on scene<br />
** no way to filter display of models or volume rendering in different viewers<br />
* Migrate fixes for oblique volume editing and threshold paint optimization after testing in trunk (Steve, Andrey)<br />
* Integrate Endoscopic layout. (Wendy)<br />
* Move Cache and DataIO manager setup out of Slicer3.cxx and into SlicerApplicationLogic (not MRML). Not done for 3.6.3 but workaround is being used. (Wendy) [http://na-mic.org/Mantis/view.php?id=1033 1033]<br />
* Debug leaks in FetchMI http://na-mic.org/Mantis/view.php?id=1029<br />
* Error messages in FetchMI: http://na-mic.org/Mantis/view.php?id=1027 (related to 1028)<br />
* Model maker pad fix http://na-mic.org/Mantis/view.php?id=813 (Nicole)<br />
* Remove bugs and simplify user interface of Extension manager: (Steve) - committed to trunk for testing<br />
** uninstall does not work <br />
** "Download /install" and "Uninstall" button should be removed and be executed via next button to keep philosophy of workflow wizard<br />
* Fix for level tracing http://na-mic.org/Mantis/view.php?id=1084<br />
* Extensions (Steve / Daniel)<br />
** Download problems http://na-mic.org/Mantis/view.php?id=1080<br />
* Migrate latest version of GrowCut into release branch (Harini)<br />
<br />
==TODO: Issues to fix for the 3.6.2 patch release Oct 22/10==<br />
<br />
<br />
<br />
=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===<br />
* Merge "reference" volume attribute feature into CommandLineModule (Andrey)<br />
* 3D Viewer does not update when slice model is visible and dragging the Fg/Bg slider [http://www.na-mic.org/Bug/view.php?id=1019 1019] (Alex)<br />
* N4 module bug in histogram sharpening parameter passing (Andrey)<br />
* Updated versions of BRAINS tools (Hans)<br />
* Detection of some BRAINS modules (e.g. BRAINSResample) (Steve)<br />
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [http://na-mic.org/Mantis/view.php?id=1032 1032]<br />
* Import does not correctly update reference [http://www.na-mic.org/Bug/view.php?id=1010 1010] (Alex)<br />
* Changing names of volume nodes is not propagated to GUI [http://www.na-mic.org/Bug/view.php?id=1012 1012] (Steve)<br />
* Editor tweaks:<br />
** add search to the color selector box - color list dynamically filtered when typing in search box<br />
** pick a new default size for the color selector box (or perhaps have it remember the last size/location picked by the user) - color box remembers size selected by user<br />
** give the color box a 'recently used' section - most recently used colors are now added at top of list for easy access<br />
** rename 'check points' to 'undo/redo'<br />
** implement compression (to vtk stencils) for label maps in the undo/redo stack (update: vtk stencils only represent a single value so they won't work for a multi-value labelmap - looking for alternatives). Done: implemented using new vtkImageStash class that uses ZLib to compress scalar image data. Also allows for compression in background thread so it does not get in the way of interactive use.<br />
* Failed memory allocation dialog box (Steve) - in slicer3 trunk<br />
* 3D Viewer disappears [http://www.na-mic.org/Bug/view.php?id=1004 1004] (Alex)<br />
* in the editor module compress saved label maps into stencils (Steve)<br />
* Side-by-side and Widescreen compare view linking problems appear fixed.<br />
* Ron requests default for crosshair to be navigator OFF <br />
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Works for nrrd, not dicom. Release note added.)<br />
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=993 (was listed as 998, but refers to duplicate bug 993] which appears to be fixed now. <br />
* FetchMI problems mentioned here [http://www.na-mic.org/Bug/view.php?id=998 998] and here [http://na-mic.org/Mantis/view.php?id=955 955] are due to (1) no or loss of network connection or (2) a full cache. (Wendy) added tests for network and server availability in fetchmi and for a full cache before attempting to transact with services. <br />
* FetchMI segfaults when uploading mrml file [http://www.na-mic.org/Bug/view.php?id=1011 1011] (Wendy: this problem is due to having no cache space. Clear the cache and make sure your filesystem has enough free space to play with, then the upload works.)<br />
* CompareView issue [http://na-mic.org/Mantis/view.php?id=929 929] (Jim)<br />
* Display tab in the volumes module should be open by default [http://www.na-mic.org/Bug/view.php?id=1001 1001]<br />
* in the editor module replace the words "Check Points" with the word "Undo" (Steve)<br />
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)<br />
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).<br />
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing): <br />
**add thumbnails to show effect of the transfer functions, <br />
**remove unneeded ones, correct a typo. <br />
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions. <br />
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)<br />
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''<br />
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)<br />
* Diffusion Tensor Glyphs not showing (Demian)<br />
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)<br />
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)<br />
* volume rendering: sampling rate and a few other tweaks (Yanling)<br />
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]<br />
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)<br />
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840<br />
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)<br />
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]<br />
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results<br />
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks<br />
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory<br />
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)<br />
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)<br />
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.<br />
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)<br />
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)<br />
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)<br />
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)<br />
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)<br />
* [https://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:GPURayCaster#Open_Issues VTK GPU Ray Cast issues] (Julien)<br />
** Flickering has not been improved since 3.6.1.<br />
** Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.<br />
* Change names of the grow cut gesture volume nodes to be consistent with the naming conventions of label map (Harini)<br />
* Grow Cut: Change the gesture volume node to be displayed on the foreground and the segmented label volume node to be displayed on the label layer of the slice views (Harini)<br />
* Grow Cut: Modify the opacities of the label layer and the foreground layer to overlay the user input gestures, the resulting segmentation on the image background (Harini)<br />
* Grow Cut: Modify user interface for setting inputs to the Grow Cut algorithm (Harini)<br />
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.2 (Steve)<br />
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)<br />
* Resolve EMSegmenter related bug in connection with BRAINSFit [http://na-mic.org/Mantis/view.php?id=1025 1025] (Dominique)<br />
* Resolved GetReferenceSubScene bugs: [http://na-mic.org/Mantis/view.php?id=1023 1023], [http://na-mic.org/Mantis/view.php?id=1031 1031], [http://na-mic.org/Mantis/view.php?id=1031 1034], [http://na-mic.org/Mantis/view.php?id=1035 1035]<br />
* Create extensions for all versions of Slicer for the release (Steve)<br />
<br />
==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==<br />
<br />
* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)<br />
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925<br />
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex). <br />
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)<br />
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)<br />
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)<br />
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)<br />
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]<br />
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)<br />
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]<br />
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.<br />
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)<br />
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.<br />
* "Change island" effect of Editor is not functioning when the Scope is set to "all"<br />
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]<br />
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851<br />
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch<br />
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch<br />
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)<br />
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)<br />
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]<br />
* EMSegment command line works now with BRAINS (Kilian)<br />
* Removed KWWidgets that do not work under Windows (Kilian)<br />
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)<br />
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])<br />
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)<br />
<br />
<br />
==3.6 Release issues==<br />
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:<br />
<br />
'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]''' <br />
<br />
*VTK GPU ray-cast clipping issue<br />
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]<br />
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]<br />
**90% of the flickering when the camera is inside the volume is removed<br />
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)<br />
<br />
*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).<br />
<br />
Done:<br />
* Remove unused color and glyph options from fiber bundle display (Alex)<br />
* fiducial behavior<br />
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)<br />
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)<br />
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch<br />
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)<br />
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])<br />
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!<br />
** done for 2d, Andras has tested it and says it's fine<br />
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)<br />
*getting BRAINS tests to pass (Hans is working on it)<br />
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).<br />
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''<br />
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''<br />
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''<br />
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)<br />
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now! <br />
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:<br />
**for Output DTI volume: DTI Volume<br />
**for Output Baseline Volume: Baseline DTI Volume<br />
**for Otsu Threshold Mask: Otsu Threshold Label Volume<br />
*new default color table (Nicole and Mike)<br />
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7<br />
** Steve and Nicole to meet June 9 to integrate default editor color table<br />
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.<br />
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)<br />
<br />
<br />
Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18075Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:36:14Z<p>Harveerar: /* Usage */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|650px|Additional edits added to the existing segmentation]]<br />
|[[Image:finalSegmentation.png|thumb|650px|Final segmentation]]<br />
|}<br />
The segmentation resulting from the user's edit is also shown.<br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different set of gestures, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===<br />
<br />
V. Vezhnevets and V. Konouchine, "GrowCut - Interactive multi-label N-D image segmentation", in Proc. Graphicon, 2005. pp. 150--156.</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18074Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:35:49Z<p>Harveerar: /* Module Description */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|650px|Additional edits added to the existing segmentation]]<br />
|[[Image:finalSegmentation.png|thumb|650px|Final segmentation]]<br />
|}<br />
The segmentation resulting from the user's edit is also shown.<br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===<br />
<br />
V. Vezhnevets and V. Konouchine, "GrowCut - Interactive multi-label N-D image segmentation", in Proc. Graphicon, 2005. pp. 150--156.</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18073Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:34:58Z<p>Harveerar: /* Module Description */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|650px|Additional edits added to the existing segmentation]]<br />
|[[Image:finalSegmentation.png|thumb|650px|Final segmentation]]<br />
|}<br />
The segmentation resulting from the user's edit are also shown.<br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===<br />
<br />
V. Vezhnevets and V. Konouchine, "GrowCut - Interactive multi-label N-D image segmentation", in Proc. Graphicon, 2005. pp. 150--156.</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18072Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:34:39Z<p>Harveerar: /* Module Description */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|350px|Additional edits added to the existing segmentation]]<br />
|[[Image:finalSegmentation.png|thumb|350px|Final segmentation]]<br />
|}<br />
The segmentation resulting from the user's edit are also shown.<br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===<br />
<br />
V. Vezhnevets and V. Konouchine, "GrowCut - Interactive multi-label N-D image segmentation", in Proc. Graphicon, 2005. pp. 150--156.</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18071Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:34:10Z<p>Harveerar: /* References */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata based on the work of [[1]]. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|350px|Additional edits added to the existing segmentation]]<br />
|[[Image:finalSegmentation.png|thumb|350px|Final segmentation]]<br />
|}<br />
The segmentation resulting from the user's edit are also shown.<br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===<br />
<br />
V. Vezhnevets and V. Konouchine, "GrowCut - Interactive multi-label N-D image segmentation", in Proc. Graphicon, 2005. pp. 150--156.</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18070Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:31:55Z<p>Harveerar: /* Module Description */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata based on the work of [[1]]. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|350px|Additional edits added to the existing segmentation]]<br />
|[[Image:finalSegmentation.png|thumb|350px|Final segmentation]]<br />
|}<br />
The segmentation resulting from the user's edit are also shown.<br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18069Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:31:15Z<p>Harveerar: /* Module Description */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata based on the work of [[1]]. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|300px|Additional edits added to the existing segmentation]]<br />
|[[Image:finalSegmentation.png|thumb|300px|Final segmentation]]<br />
|}<br />
The segmentation resulting from the user's edit are also shown.<br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18068Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:30:22Z<p>Harveerar: /* Module Name */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Input Panel]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Scribble Positive Gesture]] [[Image:inputNegGesture.png|thumb|178px|Scribble Negative Gestures]]<br />
|[[Image:segmented1.png|thumb|500px|Resulting Segmentation]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata based on the work of [[1]]. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|180px|Caption 1]]<br />
|[[Image:finalSegmentation.png|thumb|180px|Caption 2]]<br />
|}<br />
The segmentation resulting from the user's edit are also shown. <br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=File:FinalSegmentation.png&diff=18067File:FinalSegmentation.png2010-10-21T20:29:18Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:AdditionalEdit.png&diff=18066File:AdditionalEdit.png2010-10-21T20:28:50Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18065Modules:GrowCutSegmentation-Documentation-3.62010-10-21T20:28:13Z<p>Harveerar: </p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Caption 1]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Caption 2]] [[Image:inputNegGesture.png|thumb|178px|Caption 3]]<br />
|[[Image:segmented1.png|thumb|500px|Caption 4]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Editor Effect<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Harini Veeraraghavan, Jim Miller<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Grow Cut Segmentation is a competitive region growing algorithm using cellular automata based on the work of [[1]]. The algorithm works by using a set of user input scribbles for foreground and background. For N-class segmentation, the algorithm requires a set of scribbles corresponding the N classes and a scribble for a don't care class. The algorithm executes as follows:<br />
* Using the user input scribbles, the algorithm automatically computes a region of interest that encompass the scribbles. <br />
* Next, the algorithm iteratively tries to label all the pixels in the image using the label of pixels in the user scribbled portions of the image. <br />
* The algorithm converges when all the pixels in the ROI are labelled, and no pixel can change it's label any more. <br />
* Individual pixels are labeled by computing a weighted similarity metric of a pixel with all its neighbors, where the weights correspond to the neighboring pixel's strength. The neighbor that results in the largest weight greater than the given pixel's strength, confers its label to the given pixel. <br />
<br />
After the segmentation, the user can edit the segmentation by providing additional gestures in the image as illustrated in the figure below. <br />
{|<br />
|[[Image:additionalEdit.png|thumb|180px|Caption 1]]<br />
|[[Image:finalSegmentation.png|thumb|180px|Caption 2]]<br />
|}<br />
The segmentation resulting from the user's edit are also shown. <br />
<br />
== Usage ==<br />
* Scribble a set of foreground and background gestures.<br />
* Specify the input volume<br />
* Specify the output volume<br />
A gesture volume is automatically created corresponding to the output volume and is visible in the Foreground Layer. To use a different gesture, change the output volume.<br />
<br />
===Examples, Use Cases & Tutorials===<br />
* Useful for segmenting out regions of interest in a volume (image)<br />
<br />
===Quick Tour of Features and Use===<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Libs/vtkITK/itkGrowCutSegmentationImageFilter.txx]<br />
*Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Editor/GrowCutSegmentEffect.tcl]<br />
<br />
Documentation:<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=File:GrowCutPanel.png&diff=18063File:GrowCutPanel.png2010-10-21T19:53:51Z<p>Harveerar: uploaded a new version of "File:GrowCutPanel.png"</p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18062Modules:GrowCutSegmentation-Documentation-3.62010-10-21T19:52:41Z<p>Harveerar: /* Module Name */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|260px|Caption 1]]<br />
|[[Image:inputPosGesture.png|thumb|180px|Caption 2]] [[Image:inputNegGesture.png|thumb|178px|Caption 3]]<br />
|[[Image:segmented1.png|thumb|500px|Caption 4]]<br />
|}</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18061Modules:GrowCutSegmentation-Documentation-3.62010-10-21T19:52:11Z<p>Harveerar: /* Module Name */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|220px|Caption 1]]<br />
|[[Image:inputPosGesture.png|thumb|170px|Caption 2]] [[Image:inputNegGesture.png|thumb|170px|Caption 3]]<br />
|[[Image:segmented1.png|thumb|450px|Caption 4]]<br />
|}</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18060Modules:GrowCutSegmentation-Documentation-3.62010-10-21T19:51:36Z<p>Harveerar: /* Module Name */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|220px|Caption 1]]<br />
|[[Image:inputPosGesture.png|thumb|150px|Caption 2]] [[Image:inputNegGesture.png|thumb|150px|Caption 3]]<br />
|[[Image:segmented1.png|thumb|400px|Caption 4]]<br />
|}</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18059Modules:GrowCutSegmentation-Documentation-3.62010-10-21T19:51:15Z<p>Harveerar: /* Module Name */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|200px|Caption 1]]<br />
|[[Image:inputPosGesture.png|thumb|150px|Caption 2]] [[Image:inputNegGesture.png|thumb|150px|Caption 3]]<br />
|[[Image:segmented1.png|thumb|320px|Caption 4]]<br />
|}</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18058Modules:GrowCutSegmentation-Documentation-3.62010-10-21T19:50:54Z<p>Harveerar: /* Module Name */</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|200px|Caption 1]]<br />
|[[Image:inputPosGesture.png|thumb|150px|Caption 2]] [[Image:inputNegGesture.png|thumb|150px|Caption 3]]<br />
|[[Image:segmented1.png|thumb|300px|Caption 4]]<br />
|}</div>Harveerarhttps://www.slicer.org/w/index.php?title=File:GrowCutPanel.png&diff=18057File:GrowCutPanel.png2010-10-21T19:50:38Z<p>Harveerar: uploaded a new version of "File:GrowCutPanel.png"</p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:Segmented1.png&diff=18056File:Segmented1.png2010-10-21T19:44:11Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:InputNegGesture.png&diff=18055File:InputNegGesture.png2010-10-21T19:43:53Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:InputPosGesture.png&diff=18054File:InputPosGesture.png2010-10-21T19:43:16Z<p>Harveerar: uploaded a new version of "File:InputPosGesture.png"</p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:InputPosGesture.png&diff=18053File:InputPosGesture.png2010-10-21T19:41:01Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=File:GrowCutPanel.png&diff=18052File:GrowCutPanel.png2010-10-21T19:40:29Z<p>Harveerar: </p>
<hr />
<div></div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:GrowCutSegmentation-Documentation-3.6&diff=18051Modules:GrowCutSegmentation-Documentation-3.62010-10-21T19:39:52Z<p>Harveerar: Created page with '===Module Name=== Grow Cut Segmentation {| |Caption 1 |Caption 2 [[Image:inputNegGesture.png|thu…'</p>
<hr />
<div>===Module Name===<br />
Grow Cut Segmentation<br />
<br />
{|<br />
|[[Image:GrowCutPanel.png|thumb|280px|Caption 1]]<br />
|[[Image:inputPosGesture.png|thumb|280px|Caption 2]] [[Image:inputNegGesture.png|thumb|280px|Caption 3]]<br />
|[[Image:segmented1.png|thumb|280px|Caption 4]]<br />
|}</div>Harveerarhttps://www.slicer.org/w/index.php?title=Documentation/3.6&diff=18046Documentation/3.62010-10-21T18:58:25Z<p>Harveerar: /* Segmentation */</p>
<hr />
<div>[[image:Slicer3-6Announcement-v2.png| right |3.6 Icon]]<br />
=Introduction=<br />
<br />
3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications. <br />
<br />
3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.<br />
<br />
The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)<br />
<br />
The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes. The community contributing to Slicer 3.6 is [[Announcments-3.6-Team|acknowledged here]].<br />
<br />
*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.<br />
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].<br />
*For sample data see [[SampleData|here]]<br />
*For documentation on other versions of Slicer see [[Documentation|here]]<br />
*For a [[Slicer-3-6-FAQ|FAQ]] see here<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak) <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak) <br />
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)<br />
*[[Modules:StereoViewing-3.6 | Setting up and using stereoscopic viewing ]] (Curt Lisle, Wendy Plesniak)<br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)<br />
<br />
=Modules=<br />
<br />
==Core==<br />
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)<br />
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich) <br />
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)<br />
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller) <br />
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)<br />
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper) <br />
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich) <br />
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin) <br />
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)<br />
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)<br />
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich) <br />
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)<br />
<br />
==Wizards==<br />
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)<br />
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)<br />
<br />
==Informatics Modules==<br />
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) <br />
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)<br />
<br />
==Registration==<br />
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.<br />
*Fast Registration<br />
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)<br />
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller) <br />
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller) <br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen) <br />
*Robust Registration<br />
**[[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]]: automated registration (rigid to affine to nonrigid) with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)<br />
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)<br />
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).<br />
*Brain Only Registration<br />
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)<br />
*Non-Raster-Image Data Registration<br />
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)<br />
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)<br />
<br />
==Segmentation==<br />
*[[Modules:SegmentationOverview3.6|Overview]]<br />
**[[Modules:EMSegmenter-3.6|EM Segmenter]] (Kilian Pohl) <br />
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl) <br />
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching Segmentation]] (Andriy Fedorov)<br />
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)<br />
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
**[[Modules:RobustStatisticsSeg-Documentation-3.6|Robust Statistics Segmentation]] Yi Gao (yigao@gatech.edu).<br />
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).<br />
**[[Modules:GrowCutSegmentation-Documentation-3.6|Grow Cut Segmentation]] (Harini Veeraraghavan)<br />
<br />
==Quantification==<br />
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)<br />
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)<br />
<br />
==Diffusion MRI==<br />
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]<br />
* DWI Denoising<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin) <br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
* Diffusion Tensor Utilities<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) <br />
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) <br />
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)<br />
* Tractography<br />
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar) <br />
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich) <br />
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo) <br />
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)<br />
<br />
==IGT==<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)<br />
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)<br />
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)<br />
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)<br />
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)<br />
<br />
==Time Series==<br />
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)<br />
<br />
==Filtering==<br />
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)<br />
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)<br />
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)<br />
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)<br />
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) <br />
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)<br />
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen) <br />
*[[Registration:Resampling|'''Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)<br />
**[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)<br />
**[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)<br />
**[[Modules:ModelTransform-Documentation-3.6|Model Transform]]: "Resample triangulated surface models" (Alex Yarmarkovich)<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan) <br />
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan) <br />
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin) <br />
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image<br />
**[[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan) <br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)<br />
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)<br />
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao) <br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller) <br />
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)<br />
<br />
==Surface Models==<br />
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin) <br />
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)<br />
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) <br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek) <br />
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) <br />
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)<br />
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)<br />
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) <br />
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)<br />
<br />
==Converters==<br />
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)<br />
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao) <br />
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)<br />
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao) <br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Explode Volume Transform]] (Luca Antiga, Daniel Blezek)<br />
<br />
==Endoscopy==<br />
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)<br />
<br />
==Slicer Extensions==<br />
<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". They provide are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.<br />
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* The version that is available through the extension manager is chosen by the developer of that extension<br />
* Not all extensions are available on all platforms. See here for the [[Documentation-3.6:ExtensionStatus|extension status]].<br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer3:Extensions|here]].<br />
<br />
<br />
'''Available Extensions'''<br />
<br />
* Import/Export<br />
** [[Modules:PlastimatchDICOMRT|Plastimatch > DICOM-RT Import]] Greg Sharp (gcsharp@partners.org).<br />
* Segmentation<br />
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. <br />
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .<br />
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). <br />
** [[Modules:SkullStripperModule|SkullStripperModule]] '''(in progress)''' Xiaodong Tao (taox AT research.ge.com). <br />
* Registration<br />
**Robust<br />
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit) <br />
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu). <br />
*** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).<br />
* Wizards<br />
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) . <br />
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
* Tractography<br />
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).<br />
* DWI<br />
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .<br />
* Time Series<br />
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
* Quantification<br />
** [[Modules:LabelDiameterEstimation-Documentation-3.6|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)<br />
<br />
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins<br />
<br />
:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models<br />
<br />
:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface<br />
<br />
:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution<br />
<br />
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures<br />
<br />
'''Installation Instructions'''<br />
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)<br />
[[image:Slicertoolbar.png|Extensions Wizard]]<br />
<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
<br />
'''Info for Developers'''<br />
For explanations for developers see [[Slicer3:Extensions| here]]<br />
<br />
=Other information=<br />
<br />
'''Developer Tools'''<br />
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)<br />
*Note: most developer tools are not documented for end users, but contain comments in the source code<br />
<br />
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br />
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br />
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)<br />
<br />
<br />
'''Non-SPL Supported Compatibility Packages'''<br />
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''<br />
<br />
<br />
'''QA Table'''<br />
<br />
[[Slicer-3.6-QA|Slicer 3.6 QA table]]</div>Harveerarhttps://www.slicer.org/w/index.php?title=Slicer3:3.6_Final_Issues&diff=18018Slicer3:3.6 Final Issues2010-10-18T20:05:46Z<p>Harveerar: /* TODO: Issues to fix for the 3.6.2 patch release Oct 22/10 */</p>
<hr />
<div>==TODO: Issues to fix for the 3.6.3 patch release==<br />
* Integrate SPECTRE plugin as an extension (Nicole)<br />
* CompareView issue [http://na-mic.org/Mantis/view.php?id=936 936] (Jim) <br />
<br />
=== DONE: Issues fixed for inclusion in Slicer 3.6.3 ===<br />
<br />
==TODO: Issues to fix for the 3.6.2 patch release Oct 22/10==<br />
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995]<br />
* Resolve EMSegmenter related issues: (Kilian & friends)<br />
** vtkHTTPHandler is creating broken files [http://na-mic.org/Mantis/view.php?id=955 955] (Wendy)<br />
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Wendy)<br />
* in the editor module compress saved label maps into stencils (Steve)<br />
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)<br />
* [http://na-mic.org/Mantis/view.php?id=983 983] FetchMi crashes when deleting entry (Wendy --status: wendy could not reproduce; kilian has provided mrml file that demonstrates problem)<br />
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=998 998]<br />
* Katie will create a 32 bit linux version of the modules in the Extension Manager for the release (Katie->Steve)<br />
* Failed memory allocation dialog box (Steve) - in slicer3 trunk<br />
* 3D Viewer disappears [http://www.na-mic.org/Bug/view.php?id=1004 1004] (Alex)<br />
* Import does not correctly update reference [http://www.na-mic.org/Bug/view.php?id=1010 1010] (Alex)<br />
* Changing names of volume nodes is not propagated to GUI [http://www.na-mic.org/Bug/view.php?id=1012 1012] (Steve)<br />
* Change names of the grow cut gesture volume nodes to be consistent with the naming conventions of label map (Harini)<br />
* Grow Cut: Change the gesture volume node to be displayed on the foreground and the segmented label volume node to be displayed on the label layer of the slice views (Harini)<br />
* Grow Cut: Modify the opacities of the label layer and the foreground layer to overlay the user input gestures, the resulting segmentation on the image background (Harini)<br />
* Grow Cut: Modify user interface for setting inputs to the Grow Cut algorothm (Harini)<br />
=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===<br />
* FetchMI segfaults when uploading mrml file [http://www.na-mic.org/Bug/view.php?id=1011 1011] (Wendy: this problem is due to having no disk space. Clear the cache and make sure your filesystem has enough free space to play with, then the upload works.)<br />
* CompareView issue [http://na-mic.org/Mantis/view.php?id=929 929] (Jim)<br />
* Display tab in the volumes module should be open by default [http://www.na-mic.org/Bug/view.php?id=1001 1001]<br />
* in the editor module replace the words "Check Points" with the word "Undo" (Steve)<br />
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)<br />
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).<br />
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing): <br />
**add thumbnails to show effect of the transfer functions, <br />
**remove unneeded ones, correct a typo. <br />
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions. <br />
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)<br />
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''<br />
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)<br />
* Diffusion Tensor Glyphs not showing (Demian)<br />
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)<br />
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)<br />
* volume rendering: sampling rate and a few other tweaks (Yanling)<br />
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]<br />
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)<br />
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840<br />
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)<br />
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]<br />
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results<br />
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks<br />
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory<br />
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)<br />
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)<br />
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.<br />
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)<br />
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)<br />
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)<br />
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)<br />
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)<br />
* [https://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:GPURayCaster#Open_Issues VTK GPU Ray Cast issues] (Julien)<br />
** Flickering has not been improved since 3.6.1.<br />
** Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.<br />
<br />
==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==<br />
<br />
* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)<br />
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925<br />
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex). <br />
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)<br />
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)<br />
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)<br />
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)<br />
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]<br />
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)<br />
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]<br />
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.<br />
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)<br />
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.<br />
* "Change island" effect of Editor is not functioning when the Scope is set to "all"<br />
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]<br />
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851<br />
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch<br />
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch<br />
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)<br />
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)<br />
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]<br />
* EMSegment command line works now with BRAINS (Kilian)<br />
* Removed KWWidgets that do not work under Windows (Kilian)<br />
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)<br />
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])<br />
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)<br />
<br />
<br />
==3.6 Release issues==<br />
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:<br />
<br />
'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]''' <br />
<br />
*VTK GPU ray-cast clipping issue<br />
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]<br />
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]<br />
**90% of the flickering when the camera is inside the volume is removed<br />
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)<br />
<br />
*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).<br />
<br />
Done:<br />
* Remove unused color and glyph options from fiber bundle display (Alex)<br />
* fiducial behavior<br />
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)<br />
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)<br />
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch<br />
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)<br />
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])<br />
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!<br />
** done for 2d, Andras has tested it and says it's fine<br />
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)<br />
*getting BRAINS tests to pass (Hans is working on it)<br />
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).<br />
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''<br />
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''<br />
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''<br />
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)<br />
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now! <br />
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:<br />
**for Output DTI volume: DTI Volume<br />
**for Output Baseline Volume: Baseline DTI Volume<br />
**for Otsu Threshold Mask: Otsu Threshold Label Volume<br />
*new default color table (Nicole and Mike)<br />
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7<br />
** Steve and Nicole to meet June 9 to integrate default editor color table<br />
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.<br />
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)<br />
<br />
Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:MultiplyImages-Documentation-3.6&diff=15709Modules:MultiplyImages-Documentation-3.62010-05-10T20:32:25Z<p>Harveerar: /* Examples, Use Cases & Tutorials */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Multiply Images===<br />
Multiply<br />
<br />
{|<br />
|[[Image:mulpanel.png|thumb|280px|User Interface]]<br />
|[[Image:mulimage1.png|thumb|280px|Input Image 1]]<br />
[[Image:mulimage2.png|thumb|280px|Input Image 2]]<br />
|[[Image:mulresult.png|thumb|280px|Result Image]]<br />
<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Filtering.Arithmetic<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Bill Lorensen<br />
* Contact: bill.lorensen at gmail.com<br />
* Documentation: Harini Veeraraghavan<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Module performs pixel-wise multiplication of two images. The module automatically handles different resolution of the input images. The module supports input images of any data type.<br />
<br />
== Usage ==<br />
Load the input volumes(images). The default setting of the parameter Interpolation Setting is 1. For input images of the same size, this setting will work correctly. In general, its best to use input images of the same size for the multiplication operation.<br />
===Examples, Use Cases & Tutorials===<br />
This module can be used for producing intermediate results that can then be as inputs to other modules. Multiplication can also implicitly serve as a masking operation (when the portions of the image to be masked out are set to 0 in one of the input images). The example result depicted on this page, shows the multiplication of two images (input image 1) and a (input image 2) and the result depicts the input volume contained in the input image 2. Note that the multiple will produce a valid masking operation only when the regions to be masked out are 0. In general, this may not be the case and its best to use the MaskImages module.<br />
<br />
===Quick Tour of Features and Use===<br />
*"Inputs/Outputs:" This module requires two input volumes(images), and the specification of an output volume(image). The module produces an output image of the same size as the first input image. <br />
*"Parameters:" The module uses one parameter ''Interpolation Order''. The interpolation order sets the degree of B-spline interpolation to be performed on the second input image for re-sampling it to the same size as the first input image. The default setting is 1.<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
This module depends on the ITK libraries.<br />
<br />
===Dependencies===<br />
<br />
The Volumes modules is required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MultiplyTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Testing/MultiplyTest.cxx MultiplyTest.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
<!--<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]<br />
--><br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.cxx Multiply.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.xml Multiply.xml ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:MultiplyImages-Documentation-3.6&diff=15708Modules:MultiplyImages-Documentation-3.62010-05-10T20:31:49Z<p>Harveerar: /* Examples, Use Cases & Tutorials */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Multiply Images===<br />
Multiply<br />
<br />
{|<br />
|[[Image:mulpanel.png|thumb|280px|User Interface]]<br />
|[[Image:mulimage1.png|thumb|280px|Input Image 1]]<br />
[[Image:mulimage2.png|thumb|280px|Input Image 2]]<br />
|[[Image:mulresult.png|thumb|280px|Result Image]]<br />
<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Filtering.Arithmetic<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Bill Lorensen<br />
* Contact: bill.lorensen at gmail.com<br />
* Documentation: Harini Veeraraghavan<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Module performs pixel-wise multiplication of two images. The module automatically handles different resolution of the input images. The module supports input images of any data type.<br />
<br />
== Usage ==<br />
Load the input volumes(images). The default setting of the parameter Interpolation Setting is 1. For input images of the same size, this setting will work correctly. In general, its best to use input images of the same size for the multiplication operation.<br />
===Examples, Use Cases & Tutorials===<br />
This module can be used for producing intermediate results that can then be as inputs to other modules. Multiplication can also implicitly serve as a masking operation (when the portions of the image to be masked out are set to 0 in one of the input images). The example result depicted on this page, shows the multiplication of two images (input image 1) and a (input image 2) and the result depicts the input volume contained in the input image 2. Note that the masking operation will be true only when the regions to be masked out are 0. In general, this may not be the case and its best to use the MaskImages module.<br />
<br />
===Quick Tour of Features and Use===<br />
*"Inputs/Outputs:" This module requires two input volumes(images), and the specification of an output volume(image). The module produces an output image of the same size as the first input image. <br />
*"Parameters:" The module uses one parameter ''Interpolation Order''. The interpolation order sets the degree of B-spline interpolation to be performed on the second input image for re-sampling it to the same size as the first input image. The default setting is 1.<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
This module depends on the ITK libraries.<br />
<br />
===Dependencies===<br />
<br />
The Volumes modules is required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MultiplyTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Testing/MultiplyTest.cxx MultiplyTest.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
<!--<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]<br />
--><br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.cxx Multiply.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.xml Multiply.xml ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:MultiplyImages-Documentation-3.6&diff=15707Modules:MultiplyImages-Documentation-3.62010-05-10T20:27:55Z<p>Harveerar: /* Acknowledgment */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Multiply Images===<br />
Multiply<br />
<br />
{|<br />
|[[Image:mulpanel.png|thumb|280px|User Interface]]<br />
|[[Image:mulimage1.png|thumb|280px|Input Image 1]]<br />
[[Image:mulimage2.png|thumb|280px|Input Image 2]]<br />
|[[Image:mulresult.png|thumb|280px|Result Image]]<br />
<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Filtering.Arithmetic<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Bill Lorensen<br />
* Contact: bill.lorensen at gmail.com<br />
* Documentation: Harini Veeraraghavan<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Module performs pixel-wise multiplication of two images. The module automatically handles different resolution of the input images. The module supports input images of any data type.<br />
<br />
== Usage ==<br />
Load the input volumes(images). The default setting of the parameter Interpolation Setting is 1. For input images of the same size, this setting will work correctly. In general, its best to use input images of the same size for the multiplication operation.<br />
===Examples, Use Cases & Tutorials===<br />
This module can be used for producing intermediate results that can then be as inputs to other modules. Multiplication can also implicitly serve as a masking operation (when the portions of the image to be masked out are set to 0 in one of the input images). The example result depicted on this page, shows the multiplication of two images (input image 1) and a (input image 2) and the result depicts the input volume contained in the input image 2.<br />
<br />
===Quick Tour of Features and Use===<br />
*"Inputs/Outputs:" This module requires two input volumes(images), and the specification of an output volume(image). The module produces an output image of the same size as the first input image. <br />
*"Parameters:" The module uses one parameter ''Interpolation Order''. The interpolation order sets the degree of B-spline interpolation to be performed on the second input image for re-sampling it to the same size as the first input image. The default setting is 1.<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
This module depends on the ITK libraries.<br />
<br />
===Dependencies===<br />
<br />
The Volumes modules is required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MultiplyTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Testing/MultiplyTest.cxx MultiplyTest.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
<!--<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]<br />
--><br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.cxx Multiply.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.xml Multiply.xml ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is part of the National Alliance for Medical Image<br />
Computing (NAMIC), funded by the National Institutes of Health<br />
through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br />
Information on the National Centers for Biomedical Computing<br />
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:MultiplyImages-Documentation-3.6&diff=15706Modules:MultiplyImages-Documentation-3.62010-05-10T20:27:21Z<p>Harveerar: /* Examples, Use Cases & Tutorials */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Multiply Images===<br />
Multiply<br />
<br />
{|<br />
|[[Image:mulpanel.png|thumb|280px|User Interface]]<br />
|[[Image:mulimage1.png|thumb|280px|Input Image 1]]<br />
[[Image:mulimage2.png|thumb|280px|Input Image 2]]<br />
|[[Image:mulresult.png|thumb|280px|Result Image]]<br />
<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Filtering.Arithmetic<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Bill Lorensen<br />
* Contact: bill.lorensen at gmail.com<br />
* Documentation: Harini Veeraraghavan<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Module performs pixel-wise multiplication of two images. The module automatically handles different resolution of the input images. The module supports input images of any data type.<br />
<br />
== Usage ==<br />
Load the input volumes(images). The default setting of the parameter Interpolation Setting is 1. For input images of the same size, this setting will work correctly. In general, its best to use input images of the same size for the multiplication operation.<br />
===Examples, Use Cases & Tutorials===<br />
This module can be used for producing intermediate results that can then be as inputs to other modules. Multiplication can also implicitly serve as a masking operation (when the portions of the image to be masked out are set to 0 in one of the input images). The example result depicted on this page, shows the multiplication of two images (input image 1) and a (input image 2) and the result depicts the input volume contained in the input image 2.<br />
<br />
===Quick Tour of Features and Use===<br />
*"Inputs/Outputs:" This module requires two input volumes(images), and the specification of an output volume(image). The module produces an output image of the same size as the first input image. <br />
*"Parameters:" The module uses one parameter ''Interpolation Order''. The interpolation order sets the degree of B-spline interpolation to be performed on the second input image for re-sampling it to the same size as the first input image. The default setting is 1.<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
This module depends on the ITK libraries.<br />
<br />
===Dependencies===<br />
<br />
The Volumes modules is required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MultiplyTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Testing/MultiplyTest.cxx MultiplyTest.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
<!--<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]<br />
--><br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.cxx Multiply.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.xml Multiply.xml ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===</div>Harveerarhttps://www.slicer.org/w/index.php?title=Modules:MultiplyImages-Documentation-3.6&diff=15705Modules:MultiplyImages-Documentation-3.62010-05-10T20:27:01Z<p>Harveerar: /* Examples, Use Cases & Tutorials */</p>
<hr />
<div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===Multiply Images===<br />
Multiply<br />
<br />
{|<br />
|[[Image:mulpanel.png|thumb|280px|User Interface]]<br />
|[[Image:mulimage1.png|thumb|280px|Input Image 1]]<br />
[[Image:mulimage2.png|thumb|280px|Input Image 2]]<br />
|[[Image:mulresult.png|thumb|280px|Result Image]]<br />
<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: CLI<br />
<br />
Category: Filtering.Arithmetic<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author: Bill Lorensen<br />
* Contact: bill.lorensen at gmail.com<br />
* Documentation: Harini Veeraraghavan<br />
* Contact: veerarag at ge.com<br />
<br />
===Module Description===<br />
Module performs pixel-wise multiplication of two images. The module automatically handles different resolution of the input images. The module supports input images of any data type.<br />
<br />
== Usage ==<br />
Load the input volumes(images). The default setting of the parameter Interpolation Setting is 1. For input images of the same size, this setting will work correctly. In general, its best to use input images of the same size for the multiplication operation.<br />
===Examples, Use Cases & Tutorials===<br />
This module can be used for producing intermediate results that can then be as inputs to other modules. Multiplication can also implicitly serve as a masking operation (when the portions of the image to be masked out are set to 0 in one of the input images). The example result depicted on this page, shows the multiplication of two images (input image 1) and a (input image 2) and the result depicts the input volume contained in the masked volume.<br />
<br />
===Quick Tour of Features and Use===<br />
*"Inputs/Outputs:" This module requires two input volumes(images), and the specification of an output volume(image). The module produces an output image of the same size as the first input image. <br />
*"Parameters:" The module uses one parameter ''Interpolation Order''. The interpolation order sets the degree of B-spline interpolation to be performed on the second input image for re-sampling it to the same size as the first input image. The default setting is 1.<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
This module depends on the ITK libraries.<br />
<br />
===Dependencies===<br />
<br />
The Volumes modules is required for this module's use.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* MultiplyTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Testing/MultiplyTest.cxx MultiplyTest.cxx]<br />
<br />
===Known bugs===<br />
<br />
Links to known bugs in the Slicer3 bug tracker<br />
<br />
<!--<br />
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]<br />
--><br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Links to the module's source code:<br />
<br />
Source code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.cxx Multiply.cxx ] <br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/Multiply.xml Multiply.xml ]<br />
<br />
Doxygen documentation:<br />
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===</div>Harveerar