Grundlett: Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:12:21Z

Text replacement - "\[http:\/\/wiki\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Lasso at 20:39, 27 April 2018

2018-04-27T20:39:36Z

Show changes

Lasso: /* Segmentation */

2018-04-27T20:20:02Z

Segmentation

Lasso at 19:46, 27 April 2018

2018-04-27T19:46:50Z

JChris.FillionR: /* Modules by category */

2018-03-22T05:22:17Z

Modules by category

UpdateBot: Nightly -> 4.8

2017-10-18T07:05:19Z

Nightly -> 4.8

New page

<noinclude>{{documentation/versioncheck}}</noinclude>
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{{documentation/versionlist}}

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----
Where to start ?
----
* [[New_users|Getting started]]
: Quick overview about Slicer

* [[Documentation/{{documentation/version}}/Training|Training pages]]
: Information on how to use Slicer {{documentation/version}}

* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
: Set of common questions/answers

* [https://discourse.slicer.org Discussion Forum]
: The most effective way to get help from the community


----
How to
----
* [[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}
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{{:{{FULLPAGENAME}}/SlicerApplication}}

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Modules
----

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[[Image:SlicerAnnotationsV2-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Annotations|Annotations]]
 

[[Image:DataIcon.png|32px]] [[{{FULLPAGENAME}}/Modules/Data|Data]]
 

[[Image:DataStoreIcon_128.png|32px]] [[{{FULLPAGENAME}}/Modules/DataStore|Data Store]]
 

[[Image:DICOM.png|32px]] [[{{FULLPAGENAME}}/Modules/DICOM|DICOM]]
 

[[Image:Editor.png|32px]] [[{{FULLPAGENAME}}/Modules/Editor|Editor]]
 

[[Image:Markups.png|32px]] [[{{FULLPAGENAME}}/Modules/Markups|Markups]]
 

[[Image:SlicerModels-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Models|Models]]
 

[[Image:SceneViews.png|32px]] [[{{FULLPAGENAME}}/Modules/SceneViews|Scene Views]]
 

[[Image:Segmentations.png|32px]] [[{{FULLPAGENAME}}/Modules/Segmentations|Segmentations]]
 

[[Image:SegmentEditor.png|32px]] [[{{FULLPAGENAME}}/Modules/SegmentEditor|Segment Editor]]
 

[[Image:Transforms.png|32px]] [[{{FULLPAGENAME}}/Modules/Transforms|Transforms]]
 

[[Image:ViewControllersIcon.png|32px]] [[{{FULLPAGENAME}}/Modules/ViewControllers|View Controllers]]
 

[[Image:VolumeRendering.png|32px]] [[{{FULLPAGENAME}}/Modules/VolumeRendering|Volume Rendering]]
 

[[Image:SlicerVolume-Small.png|32px]] [[{{FULLPAGENAME}}/Modules/Volumes|Volumes]]
 

[[Image:Welcome.png|32px]] [[{{FULLPAGENAME}}/Modules/Welcome|Welcome to Slicer]]
 

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{{:{{FULLPAGENAME}}/ModuleExtensionListing/TOC}}

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----
Developers Corner
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]{{updated}}
: Source code, contribute patch, develop modules


----
Miscellaneous
----


* [[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]
: Slicer user documentation principle and guidelines

* [[Slicer4:VisualBlog|Visual blog]]
: Set of screenshots showing Slicer in action.

* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]
: Platform specific issues and considerations

* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]]

* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Registration/RegistrationLibrary Registration Library]
: Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.

----
Documentation in other languages
----
{{:{{FULLPAGENAME}}/Lang/ES}}

|}



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{{:{{FULLPAGENAME}}/ModuleExtensionListing/Extensions_by_name}}

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= Modules by category =

== Converters ==
* [[Documentation/Nightly/Modules/CropVolume|CropVolume]] (loadable)
* [[Documentation/Nightly/Modules/OrientScalarVolume|OrientScalarVolume]] (cli)
* [[Documentation/Nightly/Modules/VectorToScalarVolume|VectorToScalarVolume]] (scripted)
* [[Documentation/Nightly/Modules/CreateDICOMSeries|CreateDICOMSeries]] (cli)

== Developer Tools ==
* [[Documentation/Nightly/Modules/Cameras|Cameras]] (loadable)
* [[Documentation/Nightly/Modules/ExecutionModelTour|ExecutionModelTour]] (cli)
* [[Documentation/Nightly/Modules/ExtensionWizard|ExtensionWizard]] (scripted)
* [[Documentation/Nightly/Modules/EventBroker|EventBroker]]
* DoubleArrays (loadable)

=== DICOM Plugins ===
* DICOMParametricMapPlugin
* DicomUltrasoundPlugin
* DICOMSegmentationPlugin
* DICOMSlicerDataBundlePlugin
* DICOMTID1500Plugin
* [[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]
* DICOMScalarVolumePlugin
* DICOMDiffusionVolumePlugin
* DICOMLongitudinalPETCTPlugin
* DicomSroImportPlugin
* [[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]
* DicomRtImportExportPlugin
* MultiVolumeImporterPlugin
== Diffusion ==
* [[Documentation/Nightly/Modules/DMRIInstall|DMRIInstall]] (scripted)

=== Diffusion Data Conversion ===
* DWIConvert (cli)

=== Diffusion Weighted Images ===
* BRAINSDWICleanup (cli)

=== Import and Export ===
* DWIConvert (cli)

=== Utilities ===
* BRAINSDWICleanup (cli)
* [[Documentation/Nightly/Modules/ResampleDTIVolume|ResampleDTIVolume]] (cli)
* [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] (cli)

== Endoscopy ==
* [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted)

== Filter ==
* IslandRemoval (cli)

== Filtering ==
* [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBiasFieldCorrection]] (cli)
* [[Documentation/Nightly/Modules/ImageLabelCombine|ImageLabelCombine]] (cli)
* [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|VotingBinaryHoleFillingImageFilter]] (cli)
* [[Documentation/Nightly/Modules/CheckerBoardFilter|CheckerBoardFilter]] (cli)
* [[Documentation/Nightly/Modules/ExtractSkeleton|ExtractSkeleton]] (cli)
* [[Documentation/Nightly/Modules/SimpleFilters|SimpleFilters]] (scripted)
* [[Documentation/Nightly/Modules/ThresholdScalarVolume|ThresholdScalarVolume]] (cli)
* [[Documentation/Nightly/Modules/HistogramMatching|HistogramMatching]] (cli)

=== Arithmetic ===
* [[Documentation/Nightly/Modules/MultiplyScalarVolumes|MultiplyScalarVolumes]] (cli)
* [[Documentation/Nightly/Modules/AddScalarVolumes|AddScalarVolumes]] (cli)
* [[Documentation/Nightly/Modules/MaskScalarVolume|MaskScalarVolume]] (cli)
* [[Documentation/Nightly/Modules/SubtractScalarVolumes|SubtractScalarVolumes]] (cli)
* [[Documentation/Nightly/Modules/CastScalarVolume|CastScalarVolume]] (cli)

=== Denoising ===
* [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|CurvatureAnisotropicDiffusion]] (cli)
* [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|GradientAnisotropicDiffusion]] (cli)
* [[Documentation/Nightly/Modules/MedianImageFilter|MedianImageFilter]] (cli)
* [[Documentation/Nightly/Modules/GaussianBlurImageFilter|GaussianBlurImageFilter]] (cli)

=== Morphology ===
* [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|GrayscaleFillHoleImageFilter]] (cli)
* [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|GrayscaleGrindPeakImageFilter]] (cli)

== IGT ==
* [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] (loadable)

== Informatics ==
* [[Documentation/Nightly/Modules/SEG2NRRD|SEG2NRRD]] (cli)
* [[Documentation/Nightly/Modules/Tables|Tables]] (loadable)
* [[Documentation/Nightly/Modules/Data|Data]] (loadable)
* DumpSEGFrame (cli)
* Terminologies (loadable)
* [[Documentation/Nightly/Modules/Units|Units]] (loadable)
* [[Documentation/Nightly/Modules/DICOM|DICOM]] (scripted)
* [[Documentation/Nightly/Modules/SampleData|SampleData]] (scripted)
* [[Documentation/Nightly/Modules/Colors|Colors]] (loadable)
* [[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable)
* [[Documentation/Nightly/Modules/Markups|Markups]] (loadable)
* [[Documentation/Nightly/Modules/SubjectHierarchy|SubjectHierarchy]] (loadable)

=== Converters ===
* [[Documentation/Nightly/Modules/EncodeSEG|EncodeSEG]] (cli)

== Legacy ==

=== Converters ===
* [[Documentation/Nightly/Modules/BSplineToDeformationField|BSplineToDeformationField]] (cli)

=== Filtering ===
* [[Documentation/Nightly/Modules/OtsuThresholdImageFilter|OtsuThresholdImageFilter]] (cli)
* [[Documentation/Nightly/Modules/ResampleScalarVolume|ResampleScalarVolume]] (cli)

=== Registration ===
* TestGridTransformRegistration (cli)
* [[Documentation/Nightly/Modules/ExpertAutomatedRegistration|ExpertAutomatedRegistration]] (cli)
== MultiVolume Support ==
* [[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolumeImporter]] (scripted)
* [[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolumeExplorer]] (loadable)

== Quantification ==
* [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandardUptakeValueComputation]] (cli)
* SegmentStatistics (scripted)
* [[Documentation/Nightly/Modules/LabelStatistics|LabelStatistics]] (scripted)
* BRAINSLabelStats (cli)
* [[Documentation/Nightly/Modules/DataProbe|DataProbe]] (scripted)

== Registration ==
* [[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable)
* BRAINSResize (cli)
* PerformMetricTest (cli)
* [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] (scripted)
* [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] (cli)
* [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] (cli)

=== Specialized ===
* [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] (cli)
* [[Documentation/Nightly/Modules/FiducialRegistration|FiducialRegistration]] (cli)
* [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemonWarp]] (cli)
* [[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable)
* VBRAINSDemonWarp (cli)

== Segmentation ==
* EMSegmentQuick (loadable)
* [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]] (scripted)
* [[Documentation/Nightly/Modules/Editor|Editor]] (scripted)
* [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]] (cli)
* [[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable)

=== Specialized ===
* BRAINSROIAuto (cli)
* [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|RobustStatisticsSegmenter]] (cli)
* EMSegmentCommandLine (cli)

== Surface Models ==
* [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]] (scripted)
* [[Documentation/Nightly/Modules/GrayscaleModelMaker|GrayscaleModelMaker]] (cli)
* [[Documentation/Nightly/Modules/ModelMaker|ModelMaker]] (cli)
* [[Documentation/Nightly/Modules/ModelToLabelMap|ModelToLabelMap]] (cli)
* [[Documentation/Nightly/Modules/MergeModels|MergeModels]] (cli)
* [[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMapSmoothing]] (cli)
* [[Documentation/Nightly/Modules/ProbeVolumeWithModel|ProbeVolumeWithModel]] (cli)

== Utilities ==
* [[Documentation/Nightly/Modules/ScreenCapture|ScreenCapture]] (scripted)
* [[Documentation/Nightly/Modules/DataStore|DataStore]] (loadable)
* DICOMPatcher (scripted)
* BRAINSStripRotation (cli)
* EMSegmentTransformToNewFormat (cli)

=== BRAINS ===
* BRAINSTransformConvert (cli)

== Wizards ==
* [[Documentation/Nightly/Modules/CompareVolumes|CompareVolumes]] (scripted)

|}

@@ Line 306: / Line 306: @@
 == Segmentation ==
 * EMSegmentQuick    <small>(loadable)</small>
-* [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]]    <small>(scripted)</small>
+* [http://slicer.readthedocs.io/en/latest/user_guide/module_segmenteditor.html Segment Editor]    <small>(scripted)</small>
 * [[Documentation/Nightly/Modules/Editor|Editor]]    <small>(scripted)</small>
 * [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]]    <small>(cli)</small>
@@ Line 316: / Line 316: @@
 * EMSegmentCommandLine    <small>(cli)</small>
 <span id='Modules_by_category_Surface_Models'></span>
 == Surface Models ==
 * [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]]    <small>(scripted)</small>

@@ Line 79: / Line 79: @@
 <br/>
-[[Image:SegmentEditor.png|32px]] [[{{FULLPAGENAME}}/Modules/SegmentEditor|Segment Editor]]
+[[Image:SegmentEditor.png|32px]] [http://slicer.readthedocs.io/en/latest/user_guide/module_segmenteditor.html Segment Editor]
 <br/>

@@ Line 289: / Line 289: @@
 <span id='Modules_by_category_Registration'></span>
 == Registration ==
 * [[Documentation/Nightly/Modules/Transforms|Transforms]]    <small>(loadable)</small>
 * BRAINSResize    <small>(cli)</small>