Slicer Wiki - User contributions [en]

Documentation/3.6

2010-04-13T02:26:05Z

Awiles: /* IGT */

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation]] (Peter Karasev)
* Subvolume extraction with ROI widget (Andriy Fedorov)
* Registration Metrics (HD and DSC) (Haytham Elhawary)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']]
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) '''3.6 In Progress'''

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) '''Not yet 3.6'''
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''

===Registration===
*[[Slicer3:Registration|Overview of all Registration Modules ]]
*Fast
**[[Modules:Transforms-Documentation-3.6| Transforms Module for interactive rigid registration]] (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Deformable B-Spline Registration]] (Bill Lorensen) '''in progress'''
*Robust
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Register Images Robust Affine]] (Casey Goodlett)
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial-Based Registration]] (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*Experimental and auxiliary
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett)
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]] (Nicole Aucoin)
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''

===Segmentation===
*Overview (Kilian)
**[[Modules:EMSegment|EM Segment]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Simple|EM Segment Simple]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''

===Diffusion MRI===
*Diffusion MRI
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

===Time Series===
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Nicole Aucoin, Bill Lorensen) '''Not yet 3.6'''
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the icon to start the extensions wizard
[[image:ExtensionsWizard.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography

* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to IGT.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins, Daniel Haehn (haehn@bwh.harvard.edu)

* [[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models, Daniel Haehn (haehn@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''

* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution, Daniel Haehn (haehn@bwh.harvard.edu)

* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures, Daniel Haehn (haehn@bwh.harvard.edu)

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Modules:IGTToolSelector-Documentation-3.5

2010-03-25T19:10:53Z

Awiles:

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
IGTToolSelector



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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module allows you to change the model of a tracked tool for image-guided therapy. Used with the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]], a vtkPolyData model can be assigned to a transformation from the tracking system. This module has PolyData models for a needle and a probe. The user can also choose to toggle on/off (i) the target (tip) location and (ii) the tool projection. It is assumed that the projection of the tool is in the negative ''z''-direction.

== Usage ==

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

* This is intended for IGT applications where virtual representation of the surgical tool is needed for interaction with an image. Currently, this module is limited to a single tool but plans are in place to expand it to multiple tools.

===Quick Tour of Features and Use===

* '''Tool Properties Panel:'''
** Probe Transform: Select the MRML node that contains the probe transform being served up from the tracking system via the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]].
** Tool Type List: Select the tool type being tracked. Currently only three types are available: the OpenIGTLink Default, Needle and a Pointer Probe. It is easy to added other models by adding functions to the Logic code.
** Enable Tool PolyDdata Checkbox: Toggle the tool on and off.
** Show Axes Checkbox: Toggle the tool axes on and off.
** Show Tool Projection: Toggle the projection line on and off.
** Set Projection Length Slider: Control the length of the projection line. 250mm is the maximum (Is this reasonable?).
** Set Projection Diamater Slider: Control the size of the radius of the projection line. 10mm is the maximum.
** Show Tool Tip Location Checkbox: Toggle the tool tip sphere on and off.
** Set Tool Tip Diameter Slider: Control the size of the sphere at the tool tip location. 10mm is the maximum.

== Development ==

===Dependencies===

* None are needed, but you will need a transform either from OpenIGTLink or somewhere else. If you just want to test the module. Create a new transform using the [[Modules:Transforms-Documentation-3.4| Transforms Module]] and leave as the identity and assign that transform as the Probe Transform in this module.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorGUI.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorGUI.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorLogic.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorLogic.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkIGTToolSelectorGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkIGTToolSelectorLogic]

== More Information ==

===Acknowledgment===
Developed at Northern Digital Inc. (NDI). Thanks to Chris Wedlake and John Moore at the [http://www.robarts.ca Robarts Research Institute] and the [http://www.uwo.ca University of Western Ontario] for providing their code from the Atamai Viewer for the needle and pointer probe tools.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:IGTToolSelector-Documentation-3.6

2010-03-25T19:10:21Z

Awiles: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== IGTToolSelector <!-- {| |[[…'

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

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

__NOTOC__
===Module Name===
IGTToolSelector



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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module allows you to change the model of a tracked tool for image-guided therapy. Used with the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]], a vtkPolyData model can be assigned to a transformation from the tracking system. This module has PolyData models for a needle and a probe. The user can also choose to toggle on/off (i) the target (tip) location and (ii) the tool projection. It is assumed that the projection of the tool is in the negative ''z''-direction.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This is intended for IGT applications where virtual representation of the surgical tool is needed for interaction with an image. Currently, this module is limited to a single tool but plans are in place to expand it to multiple tools.

Examples of the module in use:

* Example 1 -- To be completed at a later date.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1 -- to be completed at a later date.

===Quick Tour of Features and Use===

* '''Tool Properties Panel:'''
** Probe Transform: Select the MRML node that contains the probe transform being served up from the tracking system via the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]].
** Tool Type List: Select the tool type being tracked. Currently only three types are available: the OpenIGTLink Default, Needle and a Pointer Probe. It is easy to added other models by adding functions to the Logic code.
** Enable Tool PolyDdata Checkbox: Toggle the tool on and off.
** Show Axes Checkbox: Toggle the tool axes on and off.
** Show Tool Projection: Toggle the projection line on and off.
** Set Projection Length Slider: Control the length of the projection line. 250mm is the maximum (Is this reasonable?).
** Set Projection Diamater Slider: Control the size of the radius of the projection line. 10mm is the maximum.
** Show Tool Tip Location Checkbox: Toggle the tool tip sphere on and off.
** Set Tool Tip Diameter Slider: Control the size of the sphere at the tool tip location. 10mm is the maximum.

== Development ==

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

===Dependencies===

None are needed, but you will need a transform either from OpenIGTLink or somewhere else. If you just want to test the module. Create a new transform using the [[Modules:Transforms-Documentation-3.4| Transforms Module]] and leave as the identity and assign that transform as the Probe Transform in this module.

===Tests===



===Known bugs===

Links to known bugs in the Slicer3 bug tracker



===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorGUI.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorGUI.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorLogic.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorLogic.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkIGTToolSelectorGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkIGTToolSelectorLogic]

== More Information ==

===Acknowledgment===
Developed at [http://www.ndigital.com Northern Digital Inc. (NDI)]. Thanks to Chris Wedlake and John Moore at the [http://www.robarts.ca Robarts Research Institute] and the [http://www.uwo.ca University of Western Ontario] for providing their code from the Atamai Viewer for the needle and pointer probe tools.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:CollectFiducials-Documentation-3.6

2010-03-25T16:09:58Z

Awiles: /* Dependencies */

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

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

__NOTOC__
===Module Name===
Collect Fiducials

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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module is intended for use with [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]]. The main purpose of this module is to collect patient fiducial locations from an external tracking device. Once a tracking system, such as the NDI Aurora, is configured and transforms are being passed to Slicer, then this module will let a user collect the position of patient fiducials, which can then be registered using [[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration (TransformFrom Fidcucials)]].

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Given a patient with patient fiducials attached prior to imaging or appropriate anatomical landmarks, use this module to collect the locations in the tracking (or reference tool) space for registration with the fiducials or landmarks in the associated image.

Examples of the module in use:

* To be completed at a later date.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1: To be completed at a later date.
** Data Set 1: To be completed at a later date.

===Quick Tour of Features and Use===

* '''Tracker Information: Provide the Transform MRML node that contains the transform for the tool being tracked.'''
* '''Fiducial List Node Selection Panel:
**Create a new fiducial list MRML node or select an existing list.
**Select the number of fiducials to set up the table below to have the correct number of rows. The number of fiducials should correspond to the number of fiducials that are identified in the image.
**Initialize or reset the fiducial list. An easy way to know which fiducials have been collected, it is easier to set all of them to zero and then work through the table.
**Get New Measure Button: Collect the current location of the tracked tool tip.
**Save Fiducials Button: Save the fiducial locations to the fiducial list MRML node.'''

== Development ==

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

===Dependencies===

*[[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]] is needed to serve up the tracking data either via [http://www.igstk IGSTK] or a custom program that serves up OpenIGT stream data.
*Fiducial Registration Algorithm such as [[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration (TransformFromFiducials)]]module in the Registration category is needed after the fiducial markers are collected.

===Tests===



===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* None. 

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsLogic]

== More Information ==

===Acknowledgment===
Developed at [http://www.ndigital.com Northern Digital Inc. (NDI)]

===References===

Modules:CollectFiducials-Documentation-3.6

2010-03-25T16:09:17Z

Awiles: /* Module Description */

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

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

__NOTOC__
===Module Name===
Collect Fiducials

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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module is intended for use with [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]]. The main purpose of this module is to collect patient fiducial locations from an external tracking device. Once a tracking system, such as the NDI Aurora, is configured and transforms are being passed to Slicer, then this module will let a user collect the position of patient fiducials, which can then be registered using [[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration (TransformFrom Fidcucials)]].

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Given a patient with patient fiducials attached prior to imaging or appropriate anatomical landmarks, use this module to collect the locations in the tracking (or reference tool) space for registration with the fiducials or landmarks in the associated image.

Examples of the module in use:

* To be completed at a later date.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1: To be completed at a later date.
** Data Set 1: To be completed at a later date.

===Quick Tour of Features and Use===

* '''Tracker Information: Provide the Transform MRML node that contains the transform for the tool being tracked.'''
* '''Fiducial List Node Selection Panel:
**Create a new fiducial list MRML node or select an existing list.
**Select the number of fiducials to set up the table below to have the correct number of rows. The number of fiducials should correspond to the number of fiducials that are identified in the image.
**Initialize or reset the fiducial list. An easy way to know which fiducials have been collected, it is easier to set all of them to zero and then work through the table.
**Get New Measure Button: Collect the current location of the tracked tool tip.
**Save Fiducials Button: Save the fiducial locations to the fiducial list MRML node.'''

== Development ==

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

===Dependencies===

*[[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]] is needed to serve up the tracking data either via [http://www.igstk IGSTK] or a custom program that serves up OpenIGT stream data.
*Fiducial Registration Algorithm such as TransformFromFiducials (no Wiki page found for it) module in the Registration category is needed after the fiducial markers are collected.

===Tests===



===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* None. 

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsLogic]

== More Information ==

===Acknowledgment===
Developed at [http://www.ndigital.com Northern Digital Inc. (NDI)]

===References===

Modules:CollectFiducials-Documentation-3.6

2010-03-25T16:07:09Z

Awiles: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== Collect Fiducials == Genera…'

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

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

__NOTOC__
===Module Name===
Collect Fiducials

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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module is intended for use with [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]]. The main purpose of this module is to collect patient fiducial locations from an external tracking device. Once a tracking system, such as the NDI Aurora, is configured and transforms are being passed to Slicer, then this module will let a user collect the position of patient fiducials, which can then be registered using TransformFromFiducials Module (no Wiki page exists).

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Given a patient with patient fiducials attached prior to imaging or appropriate anatomical landmarks, use this module to collect the locations in the tracking (or reference tool) space for registration with the fiducials or landmarks in the associated image.

Examples of the module in use:

* To be completed at a later date.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1: To be completed at a later date.
** Data Set 1: To be completed at a later date.

===Quick Tour of Features and Use===

* '''Tracker Information: Provide the Transform MRML node that contains the transform for the tool being tracked.'''
* '''Fiducial List Node Selection Panel:
**Create a new fiducial list MRML node or select an existing list.
**Select the number of fiducials to set up the table below to have the correct number of rows. The number of fiducials should correspond to the number of fiducials that are identified in the image.
**Initialize or reset the fiducial list. An easy way to know which fiducials have been collected, it is easier to set all of them to zero and then work through the table.
**Get New Measure Button: Collect the current location of the tracked tool tip.
**Save Fiducials Button: Save the fiducial locations to the fiducial list MRML node.'''

== Development ==

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

===Dependencies===

*[[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]] is needed to serve up the tracking data either via [http://www.igstk IGSTK] or a custom program that serves up OpenIGT stream data.
*Fiducial Registration Algorithm such as TransformFromFiducials (no Wiki page found for it) module in the Registration category is needed after the fiducial markers are collected.

===Tests===



===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* None. 

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsLogic]

== More Information ==

===Acknowledgment===
Developed at [http://www.ndigital.com Northern Digital Inc. (NDI)]

===References===

Documentation/3.6

2010-03-25T15:57:57Z

Awiles:

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]]
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]]
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]]
*[[Modules:Loading-Data-3.6| Data Loading Details]]
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]]
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]]
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors
* Atlas Creator (Sylvain Jaume)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Gyri Contour Segmentation]] (Peter Karasev)
* Subvolume extraction with ROI widget (Andriy Fedorov)
* Registration Metrics (HD and DSC) (Haytham Elhawary)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)

=List of pre-existing Modules=
==Core==
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''
*[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) transition '''Not yet 3.6'''

===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''

===Registration===
*[[Slicer3:Registration|Overview of all Registration Modules ]]
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''
**[[Modules:RegisterImagesMultiRes-Documentation-3.5|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''

===Segmentation===
*Overview (Kilian)
**[[Modules:EMSegment|EM Segment]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:EMSegment-Simple|EM Segment Simple]] (Kilian Pohl) '''Not yet 3.6'''
**[[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''
**[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''
*Analysis

====Tractography====
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles) '''Not yet 3.6'''

===Time Series===
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''

===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
*[[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the icon to start the extensions wizard
[[image:ExtensionsWizard.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''

* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com) '''Not yet 3.6'''

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''

* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu) '''Not yet 3.6'''

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry '''Not yet 3.6'''

* [[Modules:DiffusionWarp|DiffusionWarp]] '''Not yet 3.6'''

* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''

* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''

* [[Modules:LocalRegionSeg|LocalRegionSeg]] '''Not yet 3.6'''

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''

* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''

* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''

* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) '''Not yet 3.6'''

* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''

* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''

* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''

* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Deprecated Extensions'''

* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Modules:IGTToolSelector-Documentation-3.5

2010-03-18T20:21:01Z

Awiles:

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
IGTToolSelector



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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module allows you to change the model of a tracked tool for image-guided therapy. Used with the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]], a vtkPolyData model can be assigned to a transformation from the tracking system. This module has PolyData models for a needle and a probe. The user can also choose to toggle on/off (i) the target (tip) location and (ii) the tool projection. It is assumed that the projection of the tool is in the negative ''z''-direction.

== Usage ==

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

* This is intended for IGT applications where virtual representation of the surgical tool is needed for interaction with an image. Currently, this module is limited to a single tool but plans are in place to expand it to multiple tools.

===Quick Tour of Features and Use===

* '''Tool Properties Panel:'''
** Probe Transform: Select the MRML node that contains the probe transform being served up from the tracking system via the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]].
** Tool Type List: Select the tool type being tracked. Currently only three types are available: the OpenIGTLink Default, Needle and a Pointer Probe. It is easy to added other models by adding functions to the Logic code.
** Enable Tool PolyDdata Checkbox: Toggle the tool on and off.
** Show Axes Checkbox: Toggle the tool axes on and off.
** Show Tool Projection: Toggle the projection line on and off.
** Set Projection Length Slider: Control the length of the projection line. 250mm is the maximum (Is this reasonable?).
** Set Projection Diamater Slider: Control the size of the radius of the projection line. 10mm is the maximum.
** Show Tool Tip Location Checkbox: Toggle the tool tip sphere on and off.
** Set Tool Tip Diameter Slider: Control the size of the sphere at the tool tip location. 10mm is the maximum.

== Development ==

===Dependencies===

* None are needed, but you will need a transform either from OpenIGTLink or somewhere else. If you just want to test the module. Create a new transform using the [[Modules:Transforms-Documentation-3.4| Transforms Module]] and leave as the identity and assign that transform as the Probe Transform in this module.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following links for your module:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorGUI.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorGUI.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorLogic.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/IGTToolSelector/ vtkIGTToolSelectorLogic.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkIGTToolSelectorGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkIGTToolSelectorLogic]

== More Information ==

===Acknowledgment===
Developed at Northern Digital Inc. (NDI). Thanks to Chris Wedlake and John Moore at the [http://www.robarts.ca Robarts Research Institute] and the [http://www.uwo.ca University of Western Ontario] for providing their code from the Atamai Viewer for the needle and pointer probe tools.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:IGTToolSelector-Documentation-3.5

2010-03-18T20:13:00Z

Awiles:

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
IGTToolSelector



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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module allows you to change the model of a tracked tool for image-guided therapy. Used with the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]], a vtkPolyData model can be assigned to a transformation from the tracking system. This module has PolyData models for a needle and a probe. The user can also choose to toggle on/off (i) the target (tip) location and (ii) the tool projection. It is assumed that the projection of the tool is in the negative ''z''-direction.

== Usage ==

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

* This is intended for IGT applications where virtual representation of the surgical tool is needed for interaction with an image. Currently, this module is limited to a single tool but plans are in place to expand it to multiple tools.

===Quick Tour of Features and Use===

* '''Tool Properties Panel:'''
** Probe Transform: Select the MRML node that contains the probe transform being served up from the tracking system via the [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink IF Module]].
** Tool Type List: Select the tool type being tracked. Currently only three types are available: the OpenIGTLink Default, Needle and a Pointer Probe. It is easy to added other models by adding functions to the Logic code.
** Enable Tool PolyDdata Checkbox: Toggle the tool on and off.
** Show Axes Checkbox: Toggle the tool axes on and off.
** Show Tool Projection: Toggle the projection line on and off.
** Set Projection Length Slider: Control the length of the projection line. 250mm is the maximum (Is this reasonable?).
** Set Projection Diamater Slider: Control the size of the radius of the projection line. 10mm is the maximum.
** Show Tool Tip Location Checkbox: Toggle the tool tip sphere on and off.
** Set Target Diameter Slider: Control the size of the sphere at the tool tip location. 10mm is the maximum.

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following links for your module:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:IGTToolSelector-Documentation-3.5

2010-03-18T19:51:03Z

Awiles: Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Module Name=== IGTToolSelector == General …'

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
IGTToolSelector

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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Author1: Affiliation & logo, if desired
* Contributor1: Affiliation & logo, if desired
* Contributor2: Affiliation & logo, if desired
* Contact: name, email

===Module Description===
Overview of what the module does goes here.

== Usage ==

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

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

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

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following links for your module:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Documentation/3.5

2010-03-18T19:46:14Z

Awiles:

=Main GUI=

==Main GUI==
*[[Modules:MainApplicationGUI-Documentation-3.5| Main Application GUI]]
*[[Modules:EventBindings-3.5| "Hot-keys" and Keyboard Shortcuts]]
*[[Modules:DataModule-3.5| Loading Scenes and Individual Datasets through the Data Module]]
*[[Modules:Loading-Data-3.5| Data Loading Details]]
*[[Modules:Saving-Documentation-3.5| Saving Scenes and Data]]
*[[Modules:SceneSnapshots-3.5| Creating and Restoring Scene Snapshots]]
*[[Modules:ExtensionsManagementWizard-Documentation-3.5| Extensions Management Wizard]] (Terry G.)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]]
*See [[Documentation-3.5#Requirements for Modules|below]] for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)

= Requirements for Modules =
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|"Rons rules for tools"]]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules new to 3.5=
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume)
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda)
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda)
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov)
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev)
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov)
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin)
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett)
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles)
* [[Modules:IGTToolSelector-Documentation-3.5 | IGT Tool Selector ]] (Andrew Wiles)

=List of pre-existing Modules=
===Core===
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)
===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)
===Registration===
*[[Slicer3:Registration|Overview of all Registration Modules ]]
**[[Modules:RegisterImages-Documentation-3.5|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward)
**[[Modules:RegisterImagesMultires-Documentation-3.5|Register Images Multires]] (Casey Goodlett, Stephen Aylward)
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett)
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)
**[[Modules:DemonsRegistration-Documentation-3.5|Demons Registration]] (Tom Vercauteren, Kilian Pohl)
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)

===Segmentation===
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal)
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja Fernandez)
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal)
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal)

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
*Analysis

===Tractography===
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal)
*[[Modules:ROISelect-Documentation-3.5|ROI Select]] (Lauren O'Donnell)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)
===Filtering===
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] ( )
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen)

*Freesurfer Surface Section Extraction (Katharina Quintus)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the icon to start the extensions wizard
[[image:ExtensionsWizard.png|Extensions Wizard]]

===Listing of available plug-ins===
* VMTK (Daniel Haehn)
**You need to install the [[Modules:VMTKSlicerModule|VmtkSlicerModule]] to run any of the other three.
**[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
**[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms
**[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] - providing vessel enhancement filters to highlight vasculature or tubular structures

* [[Modules:EMDTIClustering-Documentation-3.5|EM DTI Clustering]] (Mahnaz Maddah)

* [[Modules:LabelDiameterEstimation-Documentation-3.5|Label Diameter Estimation]] (Andriy Fedorov)

* [[Modules:ABC-Documentation-3.5|ABC]] (Marcel Prastawa)
* [[Modules:HAMMER]] (GuorongWu, XiaodongTao, JimMiller, DinggangShen)

===Extensions Contact List===
This is a first pass list of extension authors; more to come!

{|
|ABC || Marcel Prastawa || prastawa@sci.utah.edu
|-
|EMFiberClusteringModule|| Mahnaz Maddah || maddah @nospam@ ge.com
|-
|BRAINSROIAuto || Greg Harris || gregory-harris @nospam@ uiowa.edu
|-
|Bubble Maker || Carlos Mendoza || carlos.sanchez.medoza @nospam@ gmail.com
|-
|Hammer Registration || Dinggang Shen || dgshen @nospam@ med.unc.edu
|-
|Lupus Lesion || Mark Scully || mscully @nospam@ mrn.org
|-
|VmtkSlicerModule || Daniel Haehn || haehn @nospam@ bwh.harvard.edu
|-
|Vmtkin3DSlicer || Daniel Haehn || haehn @nospam@ bwh.harvard.edu
|-
|BRAINSFit || Eun Young Kim || eunyoung-kim @nospam@ uiowa.edu
|-
|ARCTIC || Cedric Mathieu || ced.mathieu @nospam@ gmail.com
|}

Modules:CollectFiducials-Documentation-3.5

2010-03-18T16:35:10Z

Awiles:

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
CollectFiducials



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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module is intended for use with [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]]. The main purpose of this module is to collect patient fiducial locations from an external tracking device. Once a tracking system, such as the NDI Aurora, is configured and transforms are being passed to Slicer, then this module will let a user collect the position of patient fiducials, which can then be registered using TransformFromFiducials Module (no Wiki page exists).

== Usage ==

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

* Given a patient with patient fiducials attached prior to imaging or appropriate anatomical landmarks, use this module to collect the locations in the tracking (or reference tool) space for registration with the fiducials or landmarks in the associated image.

===Quick Tour of Features and Use===

* '''Tracker Information: Provide the Transform MRML node that contains the transform for the tool being tracked.'''
* '''Fiducial List Node Selection Panel:
**Create a new fiducial list MRML node or select an existing list.
**Select the number of fiducials to set up the table below to have the correct number of rows. The number of fiducials should correspond to the number of fiducials that are identified in the image.
**Initialize or reset the fiducial list. An easy way to know which fiducials have been collected, it is easier to set all of them to zero and then work through the table.
**Get New Measure Button: Collect the current location of the tracked tool tip.
**Save Fiducials Button: Save the fiducial locations to the fiducial list MRML node.'''

== Development ==

===Dependencies===

*[[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]] is needed to serve up the tracking data either via [http://www.igstk IGSTK] or a custom program that serves up OpenIGT stream data.
*Fiducial Registration Algorithm such as TransformFromFiducials (no Wiki page found for it) module in the Registration category is needed after the fiducial markers are collected.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following links for your module:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsGUI.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CollectFiducials/ vtkCollectFiducialsLogic.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html vtkCollectFiducialsLogic]

== More Information ==

===Acknowledgment===
Developed at Northern Digital Inc. (NDI)

===References===

Modules:CollectFiducials-Documentation-3.5

2010-03-18T16:23:37Z

Awiles:

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
CollectFiducials



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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module is intended for use with [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]]. The main purpose of this module is to collect patient fiducial locations from an external tracking device. Once a tracking system, such as the NDI Aurora, is configured and transforms are being passed to Slicer, then this module will let a user collect the position of patient fiducials, which can then be registered using TransformFromFiducials Module (no Wiki page exists).

== Usage ==

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

* Given a patient with patient fiducials attached prior to imaging or appropriate anatomical landmarks, use this module to collect the locations in the tracking (or reference tool) space for registration with the fiducials or landmarks in the associated image.

===Quick Tour of Features and Use===

* '''Tracker Information: Provide the Transform MRML node that contains the transform for the tool being tracked.'''
* '''Fiducial List Node Selection Panel:
**Create a new fiducial list MRML node or select an existing list.
**Select the number of fiducials to set up the table below to have the correct number of rows. The number of fiducials should correspond to the number of fiducials that are identified in the image.
**Initialize or reset the fiducial list. An easy way to know which fiducials have been collected, it is easier to set all of them to zero and then work through the table.
**Get New Measure Button: Collect the current location of the tracked tool tip.
**Save Fiducials Button: Save the fiducial locations to the fiducial list MRML node.'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following links for your module:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:CollectFiducials-Documentation-3.5

2010-03-18T16:18:29Z

Awiles: Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Module Name=== CollectFiducials <!-- {| |[…'

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
CollectFiducials



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

Type: Interactive

Category: IGT

===Authors, Collaborators & Contact===
* Andrew D. Wiles, Ph.D.: NDI (Northern Digital Inc., http://www.ndigital.com)
* Contact: awiles [at] ndigital.com

===Module Description===
This module is intended for use with [[Modules:OpenIGTLinkIF-Documentation-3.4 | OpenIGTLink Module]]. The main purpose of this module is to collect patient fiducial locations from an external tracking device. Once a tracking system, such as the NDI Aurora, is configured and transforms are being passed to Slicer, then this module will let a user collect the position of patient fiducials, which can then be registered using TransformFromFiducials Module (no Wiki page exists).

== Usage ==

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

* Given a patient with patient fiducials attached prior to imaging or appropriate anatomical landmarks, use this module to collect the locations in the tracking (or reference tool) space for registration with the fiducials or landmarks in the associated image.

===Quick Tour of Features and Use===

* '''Tracker Information: Provide the Transform MRML node that contains the transform for the tool being tracked.'''
* '''Fiducial List Node Selection Panel:
**Create a new fiducial list MRML node or select an existing list. Select the number of fiducials to set up the table. Initia '''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following links for your module:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Documentation/3.5

2010-03-18T14:24:46Z

Awiles:

=Main GUI=

==Main GUI==
*[[Modules:MainApplicationGUI-Documentation-3.5| Main Application GUI]]
*[[Modules:EventBindings-3.5| "Hot-keys" and Keyboard Shortcuts]]
*[[Modules:DataModule-3.5| Loading Scenes and Individual Datasets through the Data Module]]
*[[Modules:Loading-Data-3.5| Data Loading Details]]
*[[Modules:Saving-Documentation-3.5| Saving Scenes and Data]]
*[[Modules:SceneSnapshots-3.5| Creating and Restoring Scene Snapshots]]
*[[Modules:ExtensionsManagementWizard-Documentation-3.5| Extensions Management Wizard]] (Terry G.)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]]
*See [[Documentation-3.5#Requirements for Modules|below]] for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)

= Requirements for Modules =
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|"Rons rules for tools"]]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules new to 3.5=
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume)
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda)
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda)
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov)
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev)
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov)
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin)
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett)
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles)

=List of pre-existing Modules=
===Core===
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)
===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)
===Registration===
*[[Slicer3:Registration|Overview of all Registration Modules ]]
**[[Modules:RegisterImages-Documentation-3.5|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward)
**[[Modules:RegisterImagesMultires-Documentation-3.5|Register Images Multires]] (Casey Goodlett, Stephen Aylward)
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett)
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)
**[[Modules:DemonsRegistration-Documentation-3.5|Demons Registration]] (Tom Vercauteren)
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)

===Segmentation===
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal)
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja Fernandez)
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal)
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal)

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
*Analysis

===Tractography===
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal)
*[[Modules:ROISelect-Documentation-3.5|ROI Select]] (Lauren O'Donnell)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)
===Filtering===
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] ( )
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen)

*Freesurfer Surface Section Extraction (Katharina Quintus)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the icon to start the extensions wizard
[[image:ExtensionsWizard.png|Extensions Wizard]]

===Listing of available plug-ins===
* VMTK (Daniel Haehn)
**You need to install the [[Modules:VMTKSlicerModule|VmtkSlicerModule]] to run any of the other three.
**[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
**[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms
**[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] - providing vessel enhancement filters to highlight vasculature or tubular structures

* [[Modules:EMDTIClustering-Documentation-3.5|EM DTI Clustering]] (Mahnaz Maddah)

* [[Modules:LabelDiameterEstimation-Documentation-3.5|Label Diameter Estimation]] (Andriy Fedorov)

* [[Modules:ABC-Documentation-3.5|ABC]] (Marcel Prastawa)
* [[Modules:HAMMER]] (GuorongWu, XiaodongTao, JimMiller, DinggangShen)

===Extensions Contact List===
This is a first pass list of extension authors; more to come!

*ABC Marcel Prastawa prastawa@sci.utah.edu
*EMFiberClusteringModule Mahnaz Maddah maddah @nospam@ ge.com
*BRAINSROIAuto Greg Harris gregory-harris @nospam@ uiowa.edu
*Bubble Maker Carlos Mendoza carlos.sanchez.medoza @nospam@ gmail.com
*Hammer Registration Dinggang Shen dgshen @nospam@ med.unc.edu
*Lupus Lesion Mark Scully mscully @nospam@ mrn.org
*VmtkSlicerModule Daniel Haehn haehn @nospam@ bwh.harvard.edu
*Vmtkin3DSlicer Daniel Haehn
*BRAINSFit Eun Young Kim eunyoung-kim @nospam@ uiowa.edu
*ARCTIC Cedric Mathieu ced.mathieu @nospam@ gmail.com