Difference between revisions of "Documentation/4.0"

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(Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887)
 
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<noinclude>{{documentation/versioncheck}}</noinclude>
 
__NOTOC__
 
__NOTOC__
 
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{{documentation/versionlist}}
<!-- TODO: Create a template that will list all documentation links -->
 
<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>
 
  
 
=Table of Content=
 
=Table of Content=
Line 17: Line 16:
 
===Slicer Application===
 
===Slicer Application===
 
----
 
----
<big>
 
 
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]]
 
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]]
  
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
+
*[[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts | Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
  
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]]
+
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | '''Computer Configurations''']]
 
*[[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)
 
*[[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)
 
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. -->
 
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. -->
 
+
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
+
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
</big>
 
  
 
===Mailing Lists===
 
===Mailing Lists===
 
----
 
----
 
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]
 
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]
 +
:[http://slicer-users.65878.n3.nabble.com/ Search] in archives on nabble.com
 
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]
 
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]
 +
:[http://slicer-devel.65872.n3.nabble.com/ Search] in archives on nabble.com
  
 
<!--
 
<!--
Line 57: Line 56:
 
* [[#Developer Tools|Developer Tools]]
 
* [[#Developer Tools|Developer Tools]]
 
* [[#Legacy|Legacy]]
 
* [[#Legacy|Legacy]]
* [[#Utilities|Utility]]
 
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
Line 78: Line 76:
 
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
 
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
 
: Set of common questions/answers
 
: Set of common questions/answers
 +
 +
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]
 +
: Platform specific issues and considerations
 +
<!--
 +
* [[Documentation/{{documentation/version}}/Troubleshooting|Troubleshooting]]
 +
: Some general hints on troubleshooting,
 +
-->
  
 
===Developers Corner===
 
===Developers Corner===
 
----
 
----
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]
+
* [[Documentation/{{documentation/version}}/Developers | Information for Software Developers]]
: Handy Developer Info
+
: Where to find the source code, how to compile ...
 
|}
 
|}
  
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{{ombox
 
{{ombox
 
|type=content
 
|type=content
|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]].
+
|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 acknowledged [http://www.slicer.org/pages/Acknowledgments here].
 
}}
 
}}
 
|-
 
|-
|
+
<!--|
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}
+
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}-->
 
|}
 
|}
 
=Requirements for Modules=
 
* The module is '''feature complete''', i.e. it does everything that it advertises
 
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
 
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.
 
* 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]].
 
* Use logos listed in the [[Template:Collaborator|Collaborators Template]].
 
  
 
=Modules by Category=
 
=Modules by Category=
Line 160: Line 158:
  
 
==Registration==
 
==Registration==
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
 
*Specialized
 
*Specialized
 
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
 
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward)  
 
**Vector Demon Registration (Hans Johnson)
 
**Vector Demon Registration (Hans Johnson)
 +
**[[Documentation/4.0/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)
  
 
==Segmentation==
 
==Segmentation==
 
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)  
 
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)  
 
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)  
 
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)  
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)  
+
*[[Documentation/4.0/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)  
 
*Specialized
 
*Specialized
**[[Documentation/4.0/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum)  [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum)   
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)
+
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)
  
 
==Quantification==
 
==Quantification==
 
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
 
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
 
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
 
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)
+
*[[Documentation/4.0/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
 
* Change quantification
 
* Change quantification
 
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)
 
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)
  
 
==Diffusion==  
 
==Diffusion==  
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
*DWI to Full Brain Tractography (Demian Wasserman)  
 
*Denoising
 
*Denoising
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman)  
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman)  
 
*Tractography
 
*Tractography
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman)  
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman)  
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)  
 
*Utilities
 
*Utilities
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman)  
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)  
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman)  
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman)  
  
 
==IGT==
 
==IGT==
 +
*[[Documentation/4.0/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda)
  
 
==Filtering==
 
==Filtering==
 
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
 
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller)  
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller)  
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller)  
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)  
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin)  
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin)  
+
*[[Documentation/4.0/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)  
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller)  
*Resample Tools
 
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
 
 
*Arithmetic  
 
*Arithmetic  
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller)  
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin)  
+
**[[Documentation/4.0/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)  
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin)  
+
**[[Documentation/4.0/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)  
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller)  
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller)  
 
*Denoising
 
*Denoising
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller)
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller)  
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward)  
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller)  
 
*Morphology
 
*Morphology
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)
+
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|GGrayscale Grind Peak Image Filter]] (Jim Miller)  
  
 
==Surface Models==
 
==Surface Models==
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller)  
*Label Map Smoothing
+
*[[Documentation/4.0/Modules/LabelMapSmoothing|Label Map Smoothing]]
 
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin)  
 
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin)  
 
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)  
 
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)  
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin)  
+
*[[Documentation/4.0/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)  
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell)  
  
 
==Converters==
 
==Converters==
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller)  
 
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
 
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
 
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)  
 
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)  
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)  
  
 
==Endoscopy==
 
==Endoscopy==
Line 246: Line 244:
  
 
==Developer Tools==
 
==Developer Tools==
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet)  
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet)  
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin)  [[image:UnderConstruction.png|tumb|10px]]
+
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin)   
*Module Template
+
*[[Documentation/4.0/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Multiple Models Example
 
 
*Performance Tests
 
*Performance Tests
 
*Tractography
 
*Tractography
Line 256: Line 253:
 
==Legacy==
 
==Legacy==
 
*Converters
 
*Converters
**BSpline to Deformation Field
+
**[[Documentation/4.0/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
 
*Diffusion
 
*Diffusion
 
**Denoising
 
**Denoising
***Unbiased Non Local Means Filter for DWI
+
***[[Documentation/4.0/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
 
*Filtering
 
*Filtering
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume)  
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen)  
**Resample Scalar Volume
+
**[[Documentation/4.0/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller)
 
*Registration
 
*Registration
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller)  [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller)   
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek)  
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]]  
**Nonrigid BSpline Registration
+
**[[Documentation/4.0/Modules/ExpertAutomatedRegistration|Expert Automated Registration]]
**Expert Automated Registration
+
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]]  
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]]  
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]
+
<!--
**Robust Multiresolution Affine Registration
+
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]]  
 +
-->
 
*Segmentation
 
*Segmentation
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
+
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen)
 
 
==Utilities==
 
*Transform MRML Files to NewSegmenter Standard
 
  
 
=Extensions=
 
=Extensions=

Latest revision as of 07:36, 14 June 2013

Home < Documentation < 4.0

For the latest Slicer documentation, visit the 4.10 page.

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Table of Content

Slicer Application


Mailing Lists


Search in archives on nabble.com
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Module Categories


Miscellaneous


Set of screenshots showing Slicer in action.
Information on how to use Slicer 4.0
Set of common questions/answers
Platform specific issues and considerations

Developers Corner


Where to find the source code, how to compile ...

General Information

3D Slicer
3D Slicer 4.0
Description
Research platform for the analysis and visualization of medical images, including image guided therapy.
Free and extensible open source package.
Multi-platform Linux, MacOSX, Windows
Version 4.0
License Contribution and Software License Agreement
v · d · e

Slicer4Announcement-HiRes.png

Modules by Category

Core Modules

Wizards

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Converters

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Extensions

Introduction

  • 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.
  • 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.
  • For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
  • In case of problems with extensions, please talk directly to the developers of the extensions.
  • Information for developers can be found here. See here for the end-user documentation template.
  • 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.

Collections

Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.

id Thumbnail Name Short Description Maturity Slicer License Search terms Contact Information
1 Replace the image with your image, replace the generic documentation link with a link to your documentation MyCollection This is a collection of extensions that will do something miraculous with your images StableExtensionIcon.png SlicerLicenseIcon.png segmentation, level set my-email at mit.edu



Table Of Extensions

id Thumbnail Name Short Description Maturity Slicer License Search terms Contact Information
1 Replace the image with your image, replace the generic documentation linke with a link to your documentation MyExtension This is an extension that will do something wonderful with your data ExperimentalExtensionIcon.png NoSlicerLicenseIcon.png filter, anisotropic my-email at gmail.com
2 Replace the image with your image, replace the generic documentation linke with a link to your documentation MyExtension This is an extension that will do something miraculous with your images StableExtensionIcon.png SlicerLicenseIcon.png segmentation, level set my-email at mit.edu


Caption for the table of extensions