Documentation/4.3/Extensions

For the latest Slicer documentation, visit the read-the-docs.

Extensions by Category

Cat 2

• SkullStripper (Xiaodong Tao)
• SwissSkullStripper (Bill Lorensen)
• Cardiac MRI Toolkit (Alan Morris, Salma Bengali)
• PkModeling (Emma Zhu, Jim Miller)
• FacetedVisualizer (Harini Veeraraghavan, Jim Miller)
• Reporting (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
• SlicerRT (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)
  • DICOM-RT import
  • DICOM-RT export
  • Contours
  • Dose volume histogram
  • Dose accumulation
  • Dose comparison
  • Isodose line and surface display
  • Contour comparison
  • Contour morphology
  • Subject hierarchy
  • Modules from Plastimatch (Greg Sharp)
    • Plastimatch Automatic deformable image registration
    • Plastimatch LANDWARP Landmark
    • Plastimatch XFORMWARP
• SlicerIGT (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
  • CollectFiducials (Tamas Ungi)
  • CreateModels (Tamas Ungi, Matthew Holden)
  • OpenIGTLinkRemote (Tamas Ungi, Andras Lasso)
  • UltrasoundSnapshots (Tamas Ungi, Franklin King)
  • VolumeResliceDriver (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
• Matlab Bridge (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
• iGyne (Xiaojun Chen and iGyne Team)
• LongitudinalPETCT (Paul Mercea, Andrey Fedorov)
• DTIProcess (Francois Budin)
• DTIAtlasFiberAnalyzer (Francois Budin)
• FiberViewerLight (Francois Budin)
• DTIPrep (Francois Budin)
• DTIAtlasBuilder (Adrien Kaiser)
• ShapePopulationViewer (Alexis Girault)
• ModelToModelDistance (Francois Budin, Juliette Pera, Beatriz Paniagua)
• TubeTK (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
• UKFTractography (Ryan Eckbo, Yogesh Rathi)
• TrackerStabilizer (Laurent Chauvin, Jayender Jagadeesan)
• ChangeTracker (Andrey Fedorov)
• SobolevSegmenter (Arie Nakhmani)
• QuickTools (Julien Finet)
  • Image Maker
• XNATSlicer
• ErodeDilateLabel (Junichi)
• ThingiverseBrowser (Nigel Goh)
• Virtual Fracture Reconstruction (Karl Fritscher, Peter Karasev)
• AirwaySegmentation (Pietro Nardelli)
• ModelClip (Xiaojun Chen,Jun Lin,Qiqin Zhan)
• SurfaceMirror (Xiaojun Chen,Jiaxi Luo, Ruqing Ye)
• Scoliosis (Franklin King, Tamas Ungi)
  • Spinal Curvature Measurement (Franklin King, Tamas Ungi)
• Port Placement (Andinet Enquobahrie, Luis G. Torres)
• Plus Remote (Franklin King, Tamas Ungi)
• Transform Visualizer (Franklin King, Andras Lasso, Csaba Pinter)
• WindowLevelEffect (Andrey Fedorov, Steve Pieper)
• PerkTutor (Tamas Ungi, Matthew Holden)
  • PerkEvaluator
  • TransformRecorder
  • WorkflowSegmentation
• SlicerToKiwiExporter (Jean-Christophe Fillion-Robin)
• GelDosimetry (Csaba Pinter)
• MRI SNR Measurement (Babak Matinfar)

Cat 3

• LesionSegmentation (Mark Scully)
  • LesionSegmentation->TrainModel (Mark Scully)
  • LesionSegmentation->PredictLesions (Mark Scully)
• IASEM (Bradley Lowekamp)

User FAQ: Extensions

What is an extension ?

Extensions in the Extension manager.

An extension could be seen as a delivery package bundling together one or more Slicer modules. After installing an extension, the associated modules will be presented to the user as built-in ones

The Slicer community maintains a website referred to as the Slicer Extensions Catalog to support finding, downloading and installing of extensions. Access to this website is integral to Slicer and facilitated by the Extensions Manager functionality built into the distributed program.

The Catalog classifies extensions into three levels of compliance:

1. Category 1: Fully compliant Slicer Extensions: Slicer license, open source, maintained.
2. Category 2: Open source, contact exists.
3. Category 3: All other extensions (work in progress, beta, closed source etc).

To publish extensions, developers should consider reading the following pages:

• Bundle module(s) into a Slicer extension
• Build, test, package and distribute extensions

What is the extensions catalog ?

The extensions catalog provides Slicer users with a convenient way to access the extensions previously uploaded on the extensions server:

• from within Slicer with the help of the extensions manager
• from the web: http://slicer.kitware.com/midas3/slicerappstore

Why there are no windows 32-bit extensions available ?

• Win 32 has a very limited amount of memory available to an application.
• Many registration and segmentation algorithms fail on that platform because they run out of memory, when used with state of large data.
• Some of these failures are just that, some can crash slicer. Even though the "real" failure is caused by overextending the capabilities of the hardware (in a way the users fault), it appears to the user that Slicer does not work.
• If you search the archives of slicer-users there are several such complaints until we started to discourage people to use 32 bit.

Discussion: http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006703.html

Should I install the nightly version to access to last extension updates ?

If the extension developers contributed updates for the current stable release, you don't have to install the nightly version of Slicer. You can simply update the extension. Consider reading How to update an already installed extension ?.

On the other hand, if the extension developers stopped to maintain the version of their extension built against the stable release (so that we can use the latest feature that will be in the next Slicer release), downloading the nightly is the only way to get the latest version of the extension.

How to update an already installed extension?

Assuming updates extensions are available for your version of Slicer, it is currently not possible without uninstalling the extension and re-installing it.

We are currently developing a mechanism allowing to either manually update or automatically suggest update. In the process of finalizing, reviewing and testing, the corresponding feature will be available in Slicer 4.12.

For more details, see [1][2] and [3]

[1] http://na-mic.org/Mantis/view.php?id=2089

[2] https://github.com/mwoehlke-kitware/Slicer/tree/REBASE-2089-update-extensions

[3] http://wiki.slicer.org/wiki/Documentation/Labs/ExtensionsFrameworkRoadmap

How to manually install an extension ?

1) Get revision associated with your install or built Slicer. (Menu -> Help -> About)

2) Download extension matching your Slicer revision. Select operating system, bitness and enter revision on http://slicer.kitware.com/midas3/slicerappstore

3) Extract the archive (zip or tar.gz) in a folder. You should then have a folder like:

/path/to/<slicer_revision>-<os>-<bitness>-<extension_name>-<extension_scm><extension_revision>-YYYY-MM-DD

containing folder like:

lib/Slicer-X.Y/cli-modules
lib/Slicer-X.Y/qt-loadable-modules
lib/Slicer-X.Y/qt-scripted-modules

For more details: Documentation/4.3/Developers/DirectoryStructure

4) In the Module settings (Menu -> Edit -> Settings), add the path ending with lib/Slicer-X.Y/{cli|qt-scripted|qt-loadable}-modules