View source for Documentation/3.2

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=Introduction=
[[Image:Base-Features-and-Modules.png|thumb|right|overview]]
This page is a portal for documentation about Slicer 3.
For information for software developers, please go to the Developers page (see link in navigation box to the left).

*With the distribution of slicer3 there will be a set of bundled modules to get people started.  The exact composition of the bundled modules hasn't been finalized, but it will be similar to the current set of modules that are built in.  There may be different application-specific bundles that can optionally be loaded.  E.g. a registration bundle, an IGT bundle, a diffusion bundle, etc.

=How-To Tutorials=
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]

=Main GUI=
*[[Modules:MainApplicationGUI-Documentation-3.2| Main Application GUI]]
*[[Slicer3:EventBindings| List of Hotkeys and Keyboard Shortcuts]]
*[[Modules:Loading-Data| How to load data]]
*[[Modules:Saving-Documentation-3.2| Save Scene and Data Module]]

=Modules=
Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.2_Template|Slicer3:Module_Documentation-3.2_Template]]
==Core and Loadable Modules==
*[[Modules:Data-Documentation-3.2| Data Module]]
*[[Modules:Volumes-Documentation-3.2| Volumes Module]]
*[[Modules:DTMRI-Documentation-3.2| DTMRI Infrastructure]]
*[[Modules:Volumes:Diffusion Editor-Documentation-3.2| Diffusion Editor]]
*[[Modules:Models-Documentation-3.2| Models Module]]
*[[Modules:Modelmaker-Documentation-3.2| Modelmaker]]
*[[Modules:Transforms-Documentation-3.2| Transforms Module]]
*[[Modules:Fiducials-Documentation-3.2| Fiducials Module]]
*[[Modules:VolumeRendering-Documentation-3.2| Volume Rendering Module]]
*[[Modules:Editor-Documentation-3.2| Interactive Editor]]
*[[Slicer3:Module:QueryAtlas|Query Atlas]]
*[[Modules:EM-Segmenter-Documentation-3.2|EM Segementer]]
*[[Modules:ChangeTracker-Documentation-3.2|ChangeTracker]]

==CLI Modules==
*Registration: the top two have been somewhat tested by Ron on T1 weighted MR images and work pretty fast
*[[Modules:AffineRegistration-Documentation-3.2|Affine Registration]]
*[[Slicer3:Module:Deformable_BSpline_registration|Deformable BSpline Registration]]
*The following are somewhat undocumented and or experimental
**[[Modules:OtsuThresholding-Documentation-3.2|Otsu Thresholding]]
**[[Modules:ResampleVolume2-Documentation-3.2|Resample Volume 2]]
**[[Modules:StochasticTractography-Documentation-3.2|Stochastic Tractography]]
**[[Modules:LinearRegistration-Documentation-3.2|Linear Registration (aka rigid registration)]]
**[[Slicer3:Module:VotingBinaryHoleFilling|Voting Binary Hole Filling]]
**[[Slicer3:Module:(UTAH)Deformable_BSpline_registration|(UTAH)Deformable BSpline Registration]]
**[[Slicer3:Module:Level-Set Segmentation Framework-Documentation-3.2 |Level-Set Segmentation Framework]]
***[[Slicer3:Module:Region Selector-Documentation-3.2 |Region Selector]]
***[[Slicer3:Module:Target Preprocessing-Documentation-3.2 |Target Preprocessing]]
***[[Slicer3:Module:Bubble Maker-Documentation-3.2 |Bubble Maker]]
***[[Slicer3:Module:Level-Set Label Map Evolver-Documentation-3.2 |Level-Set Label Map Evolver]]
**[[Slicer3:Module:Binary Morphological Operations-Documentation-3.2 |Binary Morphological Operations]]
***[[Slicer3:Module:BinaryThresholding-Documentation-3.2 |BinaryThresholding]]
***[[Slicer3:Module:LabelBinaryImages-Documentation-3.2 |LabelBinaryImages]]
***[[Slicer3:Module:BinaryErodeOperations-Documentation-3.2 |BinaryErodeOperations]]
***[[Slicer3:Module:BinaryDilateOperations-Documentation-3.2 |BinaryDilateOperations]]
**[[Slicer3:Module:Fuzzy Surface Creation-Documentation-3.2 |Fuzzy Surface Creation]]

==Modules on NITRC==
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
We are using NITRC as a repository for contributed modules. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.

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 modules on NITRC.

For NITRC modules the work is still in-progress.  Active work (05/2008):
*Sebastien is working on being able to build modules based on a configuration file.  
*Terry Lorber has created GenerateLM to be used to add Loadable Module support to modules.  This allows modules to be detected and loaded at run-time.
* Terry will continue to convert Modules/* projects to use this functionality [[Slicer3:Loadable_Modules:Current]]
*Once these are done Terry will look at how to download and install new modules from places like NITRC.

Update (10/2008):

Terry is completing a prototype of the download tool that will work in conjunction with binaries hosted by NITRC.

Update (01/2009):

Extension Management Wizard prototype is complete.  As of this writing, BubbleMaker can be downloaded and enabled with this tool. Active work:
* modify program flow to follow UI draft proposal
* fixup path handling to update library paths
* allow uninstall of local modules not referenced by the extension server

==Problems and Feature Request==
We have an issues [http://www.na-mic.org/Bug/my_view_page.php tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.

==List of Modules==
*[[Modules:ChangeTracker-Documentation-3.2|ChangeTracker]]
*CommandLineModule
*DistanceMapFiducials
*DistanceTransformModel
*EMSegment
*Editor
*FetchMI
*GradientAnisotropicDiffusionFilter
*MRAblation
*Meshing (BoundingBox, VoxelMesh)
*NeuroNav
*[[Modules:OpenIGTLinkIF|OpenIGTLink IF]]
*QdecModule
*QueryAtlas
*RealTimeImaging	
*ScriptedModule
*ScriptedModuleExample
*Statistics
*Tractography (ROI, Fiducial)
*VolumeRendering
*Volumes
*WFEngineModule