Slicer Wiki - User contributions [en]

Documentation/Labs/FiberTractMeasurementAndVisualization

2015-02-24T18:35:22Z

Alexy:

= Motivation =
* Enable studies using fiber tract hierarchies to measure from many white matter structures
* Improve/Fix diffusion tractography visualization

= Features =
* Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
* Export into text file that is excel-readable
* Test and fix fiber tract visualization
* Test and fix diffusion tensor scalar measurements

= Design and implementation =

= To do lists for features and bugs =

==Fiber Tract Measurements==
* 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
* 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
* 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
* 3. Put num fibers and num points at the beginning of the list again.
* 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.
* 9. BUG: Only the first hierarchy added to the scene can be measured from.
* 12. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.] '''Status''': multi-nodes selection is currently disabled. A slicer bug filed for support of multiple node re-parenting: http://www.na-mic.org/Bug/view.php?id=3936
* 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified. Bug fixed: http://www.na-mic.org/Bug/view.php?id=3966

==Hierarchies==

==Visualization==
* 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

==Finished==
* QNAN output in cluster is ok but propagated to hierarchy is not
* Please call Num_Polylines Num_Fibers instead so users can understand.
* what is the category of the module> should be under diffusion tractography
* Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)

Documentation/Labs/FiberTractMeasurementAndVisualization

2015-02-24T17:56:45Z

Alexy:

= Motivation =
* Enable studies using fiber tract hierarchies to measure from many white matter structures
* Improve/Fix diffusion tractography visualization

= Features =
* Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
* Export into text file that is excel-readable
* Test and fix fiber tract visualization
* Test and fix diffusion tensor scalar measurements

= Design and implementation =

= To do lists for features and bugs =

==Fiber Tract Measurements==
* 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
* 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
* 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
* 3. Put num fibers and num points at the beginning of the list again.
* 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.
* 9. BUG: Only the first hierarchy added to the scene can be measured from.
* 12. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.] '''Status''': multi-nodes selection is currently disabled. A slicer bug filed for support of multiple node re-parenting: http://www.na-mic.org/Bug/view.php?id=3936

==Hierarchies==
* 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified.

==Visualization==
* 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

==Finished==
* QNAN output in cluster is ok but propagated to hierarchy is not
* Please call Num_Polylines Num_Fibers instead so users can understand.
* what is the category of the module> should be under diffusion tractography
* Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)

Documentation/Labs/FiberTractMeasurementAndVisualization

2015-02-24T17:56:04Z

Alexy: /* To be tested */

= Motivation =
* Enable studies using fiber tract hierarchies to measure from many white matter structures
* Improve/Fix diffusion tractography visualization

= Features =
* Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
* Export into text file that is excel-readable
* Test and fix fiber tract visualization
* Test and fix diffusion tensor scalar measurements

= Design and implementation =

= To do lists for features and bugs =

==Fiber Tract Measurements==
* 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
* 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
* 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
* 3. Put num fibers and num points at the beginning of the list again.
* 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.
* 9. BUG: Only the first hierarchy added to the scene can be measured from.
* 12. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.] Status: multi-nodes selection is currently disabled. A slicer bug filed for support of multiple node re-parenting: http://www.na-mic.org/Bug/view.php?id=3936

==Hierarchies==
* 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified.

==Visualization==
* 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

==Finished==
* QNAN output in cluster is ok but propagated to hierarchy is not
* Please call Num_Polylines Num_Fibers instead so users can understand.
* what is the category of the module> should be under diffusion tractography
* Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)

Documentation/Labs/FiberTractMeasurementAndVisualization

2015-02-24T17:55:43Z

Alexy:

= Motivation =
* Enable studies using fiber tract hierarchies to measure from many white matter structures
* Improve/Fix diffusion tractography visualization

= Features =
* Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
* Export into text file that is excel-readable
* Test and fix fiber tract visualization
* Test and fix diffusion tensor scalar measurements

= Design and implementation =

= To do lists for features and bugs =

==Fiber Tract Measurements==
* 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
* 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
* 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
* 3. Put num fibers and num points at the beginning of the list again.
* 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.
* 9. BUG: Only the first hierarchy added to the scene can be measured from.
* 12. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.] Status: multi-nodes selection is currently disabled. A slicer bug filed for support of multiple node re-parenting:
http://www.na-mic.org/Bug/view.php?id=3936

==Hierarchies==
* 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified.

==Visualization==
* 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

==Finished==
* QNAN output in cluster is ok but propagated to hierarchy is not
* Please call Num_Polylines Num_Fibers instead so users can understand.
* what is the category of the module> should be under diffusion tractography
* Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)

Documentation/Labs/FiberTractMeasurementAndVisualization

2015-02-20T18:59:55Z

Alexy: /* To be tested */

= Motivation =
* Enable studies using fiber tract hierarchies to measure from many white matter structures
* Improve/Fix diffusion tractography visualization

= Features =
* Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
* Export into text file that is excel-readable
* Test and fix fiber tract visualization
* Test and fix diffusion tensor scalar measurements

= Design and implementation =

= To do lists for features and bugs =

==Fiber Tract Measurements==
* 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
* 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
* 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
* 3. Put num fibers and num points at the beginning of the list again.
* 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.
* 9. BUG: Only the first hierarchy added to the scene can be measured from.

==Hierarchies==
* 9. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.]
* 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified.

==Visualization==
* 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

==Finished==
* QNAN output in cluster is ok but propagated to hierarchy is not
* Please call Num_Polylines Num_Fibers instead so users can understand.
* what is the category of the module> should be under diffusion tractography
* Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)

Documentation/Labs/FiberTractMeasurementAndVisualization

2015-02-20T18:59:33Z

Alexy: /* Fiber Tract Measurements */

= Motivation =
* Enable studies using fiber tract hierarchies to measure from many white matter structures
* Improve/Fix diffusion tractography visualization

= Features =
* Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
* Export into text file that is excel-readable
* Test and fix fiber tract visualization
* Test and fix diffusion tensor scalar measurements

= Design and implementation =

= To do lists for features and bugs =

==Fiber Tract Measurements==
* 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
* 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
* 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
* 3. Put num fibers and num points at the beginning of the list again.
* 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.

==Hierarchies==
* 9. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.]
* 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified.

==Visualization==
* 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

==Finished==
* QNAN output in cluster is ok but propagated to hierarchy is not
* Please call Num_Polylines Num_Fibers instead so users can understand.
* what is the category of the module> should be under diffusion tractography
* Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)

Documentation/Labs/FiberTractMeasurementAndVisualization

2015-01-16T19:17:28Z

Alexy:

= Motivation =
* Enable studies using fiber tract hierarchies to measure from many white matter structures
* Improve/Fix diffusion tractography visualization

= Features =
* Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
* Export into text file that is excel-readable
* Test and fix fiber tract visualization
* Test and fix diffusion tensor scalar measurements

= Design and implementation =

= To do lists for features and bugs =

==Fiber Tract Measurements==
* 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
* 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
* 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
* 3. Put num fibers and num points at the beginning of the list again.
* 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.

==Hierarchies==
* 9. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.]
* 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified.

==Visualization==
* 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

==Finished==
* QNAN output in cluster is ok but propagated to hierarchy is not
* Please call Num_Polylines Num_Fibers instead so users can understand.
* what is the category of the module> should be under diffusion tractography
* Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)

Documentation/Nightly/Announcements

2014-11-16T15:31:05Z

Alexy: /* Transforms */

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

{|width="100%"
|align="center"|
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]
|}

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Summary|Summary ]]
|[[#What is 3D Slicer|What is 3D Slicer]]
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]
|[[#Slicer Extensions|Slicer Extensions]]
|[[#Other Improvements, Additions & Documentation|Other Improvements, Additions & Documentation]]
|}

= Summary =

The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.

* Slicer {{documentation/version}} introduces
** an improved App store, known as the extension manager, for adding capabilities to Slicer. More than 50 plug-ins are currently available.
** close to 400 feature improvements and bug fixes lead to improved performance and stability.
** augmentation of many modules.

* Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker.
* Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.
* The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of courses for learning how to use Slicer. The portfolio contains self-guided presentation and sample data sets.

The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep the pages organized and up to date.

= What is 3D Slicer =
Slicer is a community platform created for the purpose of subject specific image analysis and visualization.

* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* Multi organ from head to toe
* Bidirectional interface for devices
* Expandable and interfaced to multiple toolkits

There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]

= Slicer {{documentation/version}} Highlights =

<gallery caption="New and Improved Modules" widths="350px" heights="250px" perrow="3">

Image:LandmarkRegistration-4.4.png|New [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] module providing interactive registration and inspection.

Image:SlicerRT_0.13_SubjectHierarchy_ProstateEclipseLoaded.png|New [[Documentation/Nightly/Modules/SubjectHierarchy|Subject hierarchy]] module organizes and handles loaded data, providing processing and analysis features through plugins.

Image:Grid3dSlice.png|Improved [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module with: <ul><li>Support for non-linear transforms</li><li>Display of transform information</li><li>Transform visualization</li></ul>

Image:ExtensionWizard-and-ExtensionsManager.png|New [[Documentation/{{documentation/version}}/Developers/ExtensionWizard|ExtensionsWizard]] tool deprecating the [[Documentation/{{documentation/version}}/Developers/ModuleWizard|ModuleWizard]]. <ul><li>This new tool separates the concepts of extensions and modules, and allows creating an extension containing several modules, as well as adding modules to an existing extension.</li><li>It allows to publish an extension source code to github.</li><li>It provides an easy way to create a pull request on the extension index.</li></ul>

Image:CompareVolumes-1-volume.png|New [[Documentation/{{documentation/version}}/Modules/CompareVolumes|Compare Volumes]] supports an overview of one or more volumes in the scene.
<ul>
<li>For one volume you can look at an array of equally spaced images (like [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|LightBox mode]], but wth an independent viewer per slice.</li><li>You can have a look at one viewer per loaded volume.</li><li>You can choose a common label or background volume for each per-volume viewer.</li>
<li>The RevealCursor allows you to look in detail at the fg/bg layers.</li>
</ul>
</gallery>

== DICOM ==

* Improve [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] support user experience
** Add a way to change the table densities in three levels: compact, cozy and comfortable.
** Re-arranged the patient, study and series search box so that the search box will be on the top of tables for both horizontal and vertical cases.
** Resize tables based on contents.
** Allow users to acknowledge all DICOM loading errors with a single click
** Add DICOM header viewer

== Transforms ==

* Improved integration of non rigid deformations, including Grid and BSpline transforms
* Interactive application of non rigid deformations to volume slices
* Visualization of non rigid deformations as glyphs, grid, or contours
* Allow loading of bspline transforms with IdentityTransform bulk component
* Add support for oriented grid Transform
* Add grid transform reading-writing from h5 file

== Markups ==

* Improved [[Documentation/{{documentation/version}}/Modules/Markups|Markups]] module user interface
** Add slice intersections toggle
** Add right click option to copy markups list
** Add coordinates to right click menu

== Editor ==

* Add a Sphere option to the PaintEffect to make it quicker to segment large anatomical regions that are somewhat spherical.
* Paint using pixel mode if brush size is too small
* Button effect are checked/unchecked based on the 'effect' property stored in the parameter node

== Extensions Manager ==
* Add search box
* Add 'More' link
* Load extension icon from disk
* Implement downloading of extension icons
* Install extension dependencies
* Add mechanism to check for extensions updates

=Slicer Extensions=

TODO: Will be generating automatically list.

<gallery caption="New and Improved Extensions" widths="250px" heights="150px" perrow="4">





<gallery caption="TODO - Please add entry to illustrate awesome feature listed above" widths="250px" heights="150px" perrow="3">

</gallery>

= For Developers =

== Under the hood ==

* VolumeLogic:
** Add method [http://slicer.org/doc/html/classvtkSlicerVolumesLogic.html#a1fe71cc716593ac47988e71bdee736c9 ResampleVolumeToReferenceVolume]
** Add method [http://slicer.org/doc/html/classvtkSlicerVolumesLogic.html#ab852b66dc8108a8a544b845c0e055109 CloneVolumeWithoutImageData]

* Add support for user-defined stereo-viewing options

* Build-system
** Improve support for Visual Studio 2013
** Refactor management of external project launcher settings. See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23724 r23724]
** Add option <code>Slicer_ITKV3_COMPATIBILITY</code>. This option enabled by default will allow (if disabled) to build Slicer with ITKv3 compatibility later disabled and <code>ITK_USE_64BITS_IDS</code> enabled.

* SlicerExecutionModel: Add [https://github.com/Slicer/SlicerExecutionModel/pull/20#issue-18339466 ParameterSerializer support].

<gallery caption="Improved Toolkits" widths="250px" heights="150px" perrow="3">
Image:CTK-Logo.png|Moved from CTK [https://github.com/commontk/CTK/commit/f64b68a f64b68a] to [https://github.com/commontk/CTK/commit/1c97e54 1c97e54] (499 commits) 
Image:CTKApplauncher_Logo.png|Moved from CTKAppLauncher v0.1.11 to v0.1.14 (43 commits) 
Image:ITK_logo.png|Moved from ITK v4.4.1 to v4.6.0 (1089 commits) 
Image:OpenIGTLink-Logo.png|Moved from OpenIGTLink [https://github.com/openigtlink/OpenIGTLink/compare/66e272d...849b434 66e272d to 849b434] (53 commits) 
Image:Qt-logo.png |Moved from Qt 4.7.4 to Qt 4.8.6
Image:VTK_logo.png|Moved from VTK v5.10.1 to VTK v6.2.0 (5490 commits) 
</gallery>

== Looking at the Code Changes ==

From a git checkout you can easily see the all the commits since the time of the 4.4.0 release:

git log v4.3.0..HEAD

To see a summary of your own commits, you could use something like:

git log v4.3.0..HEAD --oneline --author=pieper

see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.

[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]

= Related Projects =
<gallery caption="" widths="250px" heights="150px" perrow="3">
</gallery>

Documentation/4.3/Modules/FinslerBacktracing

2014-05-02T16:31:14Z

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Documentation/Nightly/Modules/FinslerTractography

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Alexy:

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}

Acknowledgments:
Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee 
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware). 

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.

The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles


{{documentation/{{documentation/version}}/module-section|Use Cases}}
The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). 

The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..

{{documentation/{{documentation/version}}/module-section|Tutorials}}

N/A


{{documentation/{{documentation/version}}/module-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
* GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/FinslerBacktracing

2014-05-02T16:15:42Z

Alexy:

Documentation/Nightly/Modules/FinslerBacktracing

2014-05-02T16:12:42Z

Alexy:

Documentation/Nightly/Modules/FinslerBacktracing

2014-05-02T16:09:45Z

Alexy: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}

Acknowledgments:
Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee 
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware). 

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.

The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles

{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]
*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). 

The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..

{{documentation/{{documentation/version}}/extension-section|Tutorials}}

N/A


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}
* GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/FinslerTractography

2014-05-02T16:08:37Z

Alexy:

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}

Acknowledgments:
Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee 
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware). 

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.

The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles

{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]
*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). 

The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..

{{documentation/{{documentation/version}}/extension-section|Tutorials}}

N/A


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}
* GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/FinslerTractography

2014-05-02T16:06:34Z

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}

Acknowledgments:
Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee 
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware). 

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.

The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles

{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]
*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). 

The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..

{{documentation/{{documentation/version}}/extension-section|Tutorials}}

N/A


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}
* GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions

2014-05-02T16:00:36Z

Alexy: /* Cat 2 */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Documentation/Nightly/Extensions/FinslerTractography

2014-05-02T15:55:40Z

Alexy:

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}

Acknowledgments:
Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee 
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware). 

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.

The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles

{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]
*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). 

The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..

{{documentation/{{documentation/version}}/extension-section|Tutorials}}

N/A


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}
* GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/FinslerTractography

2014-05-02T15:53:44Z

Alexy:

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}

Acknowledgments:
Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee 
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware). 

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.

The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles

{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]
*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). 

The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..

{{documentation/{{documentation/version}}/extension-section|Tutorials}}

<gallery widths="200px" perrow="4">
Image:plastimatch_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1023/3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]
Image:plastimatch_tutorial_data.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1004/rider-lung-images.tar.gz Download tutorial data]
Image:plastimatch_dicomrt_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1568/3D_Slicer_Plastimatch_DICOM_RT_Tutorial_2010_12_28.pdf Download tutorial (PDF)]
Image:plastimatch_dicomrt_ss.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz (Download tutorial data)]
Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]
Image:fixed.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}
* G Sharp, N Kandasamy, H Singh, M Folkert, "GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration," Physics in Medicine and Biology, 52(19), pp 5771-83, 2007.
* V Boldea, G Sharp, SB Jiang, D Sarrut, "4D-CT lung motion estimation with deformable registration: Quantification of motion nonlinearity and hysteresis," Medical Physics, 33(3), pp 1008-18, 2008.
* Z Wu, E Rietzel, V Boldea, D Sarrut, G Sharp, "Evaluation of deformable registration of patient lung 4DCT with sub-anatomical region segmentations," Medical Physics, 35(2), pp 775-81, 2008.
* G Sharp et al. "Plastimatch - An open source software suite for radiotherapy image processing," Proceedings of the XVIth International Conference on the use of Computers in Radiotherapy, May, 2010.
* N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/FinslerTractography

2014-05-02T15:50:23Z

Alexy:

Documentation/Nightly/Extensions/FinslerTractography

2014-05-02T15:49:36Z

Alexy:

Documentation/Nightly/Extensions/FinslerTractography

2014-05-02T15:47:11Z

Alexy:

Documentation/Nightly/Extensions/FinslerTractography

2014-05-02T15:46:23Z

Alexy:

Documentation/Nightly/Extensions/FinslerTractography

2014-05-02T15:44:10Z

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by ... 
Author:Greg Sharp 
Contributors: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Greg Sharp, <email>gcsharp@partners.org</email> 
Website: http://plastimatch.org/ 
License: [http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=browse&path=%2F*checkout*%2Fplastimatch%2Ftrunk%2Fsrc%2Fplastimatch%2FLICENSE.TXT&revision=2388 BSD]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). Software features include:

*B-spline method for deformable image registration (GPU and multicore accelerated)
*Demons method for deformable image registration (GPU accelerated)
*ITK-based algorithms for translation, rigid, affine, demons, and B-spline registration
*Pipelined, multi-stage registration framework with seamless conversion between most algorithms and transform types
*Landmark-based deformable registration using thin-plate splines for global registration
*Landmark-based deformable registration using radial basis functions for local corrections
*Broad support for 3D image file formats (using ITK), including DICOM, Nifti, NRRD, MetaImage, and Analyze
*DICOM and DICOM-RT import and export
*XiO import and export


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
[http://plastimatch.org/data_sources.html Sample data] to use with modules.
<gallery widths="200px" perrow="4">
Image:plastimatch_dicomrt_ss.png|DICOM-RT Structure Set
Image:plastimatch_dicomrt_dose.png|DICOM-RT Dose
Image:plastimatch_image_1.png|Before Registration
Image:plastimatch_image_2.png|After Registration
Image:before_reg.png|Before Registration
Image:after_reg.png|After Registration
</gallery>


{{documentation/{{documentation/version}}/extension-section|Tutorials}}

<gallery widths="200px" perrow="4">
Image:plastimatch_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1023/3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]
Image:plastimatch_tutorial_data.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1004/rider-lung-images.tar.gz Download tutorial data]
Image:plastimatch_dicomrt_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1568/3D_Slicer_Plastimatch_DICOM_RT_Tutorial_2010_12_28.pdf Download tutorial (PDF)]
Image:plastimatch_dicomrt_ss.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz (Download tutorial data)]
Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]
Image:fixed.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]
</gallery>


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}
* G Sharp, N Kandasamy, H Singh, M Folkert, "GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration," Physics in Medicine and Biology, 52(19), pp 5771-83, 2007.
* V Boldea, G Sharp, SB Jiang, D Sarrut, "4D-CT lung motion estimation with deformable registration: Quantification of motion nonlinearity and hysteresis," Medical Physics, 33(3), pp 1008-18, 2008.
* Z Wu, E Rietzel, V Boldea, D Sarrut, G Sharp, "Evaluation of deformable registration of patient lung 4DCT with sub-anatomical region segmentations," Medical Physics, 35(2), pp 775-81, 2008.
* G Sharp et al. "Plastimatch - An open source software suite for radiotherapy image processing," Proceedings of the XVIth International Conference on the use of Computers in Radiotherapy, May, 2010.
* N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Labs/NonlinearTransforms

2013-12-10T22:31:25Z

Alexy: /* Code branch on github */

= Motivation: current state of non-linear transforms in Slicer 4.2 =

Slicer 4.2 has a very limited non-linear transforms support.

* MRML nodes exist for BSpline and Grid transforms
* There is a number of CLI modules that input and output non-linear transforms
* There is no support for import/export of non-linear transforms
* There is no support in Data module for applying non-linear transforms by dragging Volumes and Models
* There is no support in Data module for hardening of non-linear transforms for Volumes and Models
* CLI modules input and output "resampling" transform, which transforms from parent space, where linear transforms are stored as "modeling" transforms, which transforms to parent space

= New features implemented in this project =

* Support for import/export of non-linear transforms
* Support in Data module for applying non-linear transforms by dragging Volumes and Models
* Support in Data module for hardening of non-linear transforms for Volumes and Models
* Support for both "to parent" and "from parent" types of transforms in MRML nodes (both linear and non-linear)
* Support for both "to world" and "from world" types of transforms in MRML nodes (both linear and non-linear)
* Support for caching of "to parent" and "from parent" types of transforms in MRML nodes (both linear and non-linear)
* Maintain backward compatibility with existing CLI modules
= MRML API changes =
== vtkMRMLTransformNode ==
* new method virtual vtkGeneralTransform*GetTransformFromParent()
* new method void GetTransformFromWorld(vtkGeneralTransform* transformToWorld)
* new flag vtkMRMLTransformNode::ReadWriteAsTransformToParent which tells storage nodes wheather to read/write transform data as from parent or to parent. The flag is implemented in vtkMRMLTransformNode to maintain backward compatibility with CLI modules that read/write non-linear transforms as “resampling” , from parent space transforms.
== vtkMRMLLinearTransformNode ==
* changed signature of the method virtual void GetMatrixTransformToParent(vtkMatrix4x4*)
* new method virtual void GetMatrixTransformFromParent(vtkMatrix4x4*);
* new method void SetAndObserveMatrixTransformFromParent(vtkMatrix4x4 *matrix);
== vtkMRMLNonlinearTransformNode ==
* changed signature of the method virtual void GeWarpTransformToParent(vtkWarpTransform*)
* new method virtual void GeWarpTransformFromParent(vtkWarpTransform*);
* new method void SetAndObserveWarpTransformFromParent(vtkWarpTransform*matrix);
== Other MRML nodes ==
* implemented above APIs in vtkMRMLBSplineTransformNode and vtkMRMLGridTransformNode
* added support for applying transforms (hardening) to Volume and Model nodes
= Support for dragging under non-linear transforms in Data module =
* vtkMRMLSliceLayerLogic class has been redesigned to deal with generic transforms rather than just vtkMatrix4x4
* vtkMRMLModelDisplayableManager class has been redesigned to deal with generic transforms rather than just vtkMatrix4x4
= Code branch on github =
https://github.com/ayarmarkovich/Slicer/tree/xform_branch

Documentation/Labs/NonlinearTransforms

2013-12-10T22:31:00Z

Alexy:

= Motivation: current state of non-linear transforms in Slicer 4.2 =

Slicer 4.2 has a very limited non-linear transforms support.

* MRML nodes exist for BSpline and Grid transforms
* There is a number of CLI modules that input and output non-linear transforms
* There is no support for import/export of non-linear transforms
* There is no support in Data module for applying non-linear transforms by dragging Volumes and Models
* There is no support in Data module for hardening of non-linear transforms for Volumes and Models
* CLI modules input and output "resampling" transform, which transforms from parent space, where linear transforms are stored as "modeling" transforms, which transforms to parent space

= New features implemented in this project =

* Support for import/export of non-linear transforms
* Support in Data module for applying non-linear transforms by dragging Volumes and Models
* Support in Data module for hardening of non-linear transforms for Volumes and Models
* Support for both "to parent" and "from parent" types of transforms in MRML nodes (both linear and non-linear)
* Support for both "to world" and "from world" types of transforms in MRML nodes (both linear and non-linear)
* Support for caching of "to parent" and "from parent" types of transforms in MRML nodes (both linear and non-linear)
* Maintain backward compatibility with existing CLI modules
= MRML API changes =
== vtkMRMLTransformNode ==
* new method virtual vtkGeneralTransform*GetTransformFromParent()
* new method void GetTransformFromWorld(vtkGeneralTransform* transformToWorld)
* new flag vtkMRMLTransformNode::ReadWriteAsTransformToParent which tells storage nodes wheather to read/write transform data as from parent or to parent. The flag is implemented in vtkMRMLTransformNode to maintain backward compatibility with CLI modules that read/write non-linear transforms as “resampling” , from parent space transforms.
== vtkMRMLLinearTransformNode ==
* changed signature of the method virtual void GetMatrixTransformToParent(vtkMatrix4x4*)
* new method virtual void GetMatrixTransformFromParent(vtkMatrix4x4*);
* new method void SetAndObserveMatrixTransformFromParent(vtkMatrix4x4 *matrix);
== vtkMRMLNonlinearTransformNode ==
* changed signature of the method virtual void GeWarpTransformToParent(vtkWarpTransform*)
* new method virtual void GeWarpTransformFromParent(vtkWarpTransform*);
* new method void SetAndObserveWarpTransformFromParent(vtkWarpTransform*matrix);
== Other MRML nodes ==
* implemented above APIs in vtkMRMLBSplineTransformNode and vtkMRMLGridTransformNode
* added support for applying transforms (hardening) to Volume and Model nodes
= Support for dragging under non-linear transforms in Data module =
* vtkMRMLSliceLayerLogic class has been redesigned to deal with generic transforms rather than just vtkMatrix4x4
* vtkMRMLModelDisplayableManager class has been redesigned to deal with generic transforms rather than just vtkMatrix4x4
== Code branch on github ==
https://github.com/ayarmarkovich/Slicer/tree/xform_branch

Documentation/Labs

2013-12-10T15:29:25Z

Alexy: /* Internals */

This is the place where we will keep track of our experiments.

= On-going =

== Internals ==
* [[{{FULLPAGENAME}}/DeprecatedModules|DeprecatedModules extension]]
* [[{{FULLPAGENAME}}/MultiDimensional Data Management|MultiDimensional Data Management]]
* [[{{FULLPAGENAME}}/NonlinearTransforms|Full support for non-linear transforms]]

== Libraries ==
* [[{{FULLPAGENAME}}/VTK6|VTK6]]

== Python ==
* [[{{FULLPAGENAME}}/CallingPythonMethodsFromCpp|Calling Python methods from Cpp]]
* [[{{FULLPAGENAME}}/IPython|IPython]]

== Compilers & IDE ==
* [[{{FULLPAGENAME}}/Ninja|Ninja]]
* [[{{FULLPAGENAME}}/VS2012|VS2012]]
* [[{{FULLPAGENAME}}/NUMPY171|Support for Numpy 1.7.1]]

== Virtual Machines ==
* [[{{FULLPAGENAME}}/GPU Virtualization|GPU Virtualization]]

== Documentation ==
* [[{{FULLPAGENAME}}/DocumentationImprovments|Documentation Improvements (Wiki, website, ...)]]

== Extension ==

* [[{{FULLPAGENAME}}/EasyExtensionContribution|Easy Extension Contribution]]

= Completed =

== Internals ==
* [[{{FULLPAGENAME}}/CMake-ified Python|CMake-ified Python]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21911 r21911], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21912 r21912], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21913 r21913]

== Libraries ==
* [[{{FULLPAGENAME}}/ITKv4|ITKv4]]
* [[{{FULLPAGENAME}}/Qt484|Qt484]]

== Python ==
* [[{{FULLPAGENAME}}/DevelopmentWithGit|Development with Git]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21863 r21863], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21867 r21867], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21869 r21869], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21879 r21879], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21891 r21891]

== Modules ==
* [[{{FULLPAGENAME}}/SimpleFilters|Simple Filters]]
* [[{{FULLPAGENAME}}/Editor|Editor]]

== Tutorials testing ==
* [[{{FULLPAGENAME}}/TutorialTesting/4.3-Release|4.3 Release]]

== Debug ==
* [[{{FULLPAGENAME}}/BRAINS_and_ITKv4_issue|BRAINS and ITKv4 issue]]

== Internals ==
* [[{{FULLPAGENAME}}/I18N|Internationalization]]
* [[{{FULLPAGENAME}}/Units|Units]]
* [https://github.com/TubeTK/SlicerExecutionModel/wiki/SlicerExecutionModel-Parameter-Serialization SlicerExecutionModel Parameter Serialization]

Documentation/Labs/NonlinearTransforms

2013-12-10T15:28:13Z

Alexy: Created page with '= Motivation: current state of non-linear transforms in Slicer 4.2 = Slicer 4.2 has a very limited non-linear transforms support. * MRML nodes exist for BSpline and Grid transf…'

Documentation/Labs

2013-12-10T14:27:45Z

Alexy: /* Internals */

This is the place where we will keep track of our experiments.

= On-going =

== Internals ==
* [[{{FULLPAGENAME}}/DeprecatedModules|DeprecatedModules extension]]
* [[{{FULLPAGENAME}}/MultiDimensional Data Management|MultiDimensional Data Management]]
* [[{{FULLPAGENAME}}/NonlinearTransforms|Incorporate non-linear transforms]]

== Libraries ==
* [[{{FULLPAGENAME}}/VTK6|VTK6]]

== Python ==
* [[{{FULLPAGENAME}}/CallingPythonMethodsFromCpp|Calling Python methods from Cpp]]
* [[{{FULLPAGENAME}}/IPython|IPython]]

== Compilers & IDE ==
* [[{{FULLPAGENAME}}/Ninja|Ninja]]
* [[{{FULLPAGENAME}}/VS2012|VS2012]]
* [[{{FULLPAGENAME}}/NUMPY171|Support for Numpy 1.7.1]]

== Virtual Machines ==
* [[{{FULLPAGENAME}}/GPU Virtualization|GPU Virtualization]]

== Documentation ==
* [[{{FULLPAGENAME}}/DocumentationImprovments|Documentation Improvements (Wiki, website, ...)]]

== Extension ==

* [[{{FULLPAGENAME}}/EasyExtensionContribution|Easy Extension Contribution]]

= Completed =

== Internals ==
* [[{{FULLPAGENAME}}/CMake-ified Python|CMake-ified Python]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21911 r21911], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21912 r21912], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21913 r21913]

== Libraries ==
* [[{{FULLPAGENAME}}/ITKv4|ITKv4]]
* [[{{FULLPAGENAME}}/Qt484|Qt484]]

== Python ==
* [[{{FULLPAGENAME}}/DevelopmentWithGit|Development with Git]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21863 r21863], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21867 r21867], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21869 r21869], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21879 r21879], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21891 r21891]

== Modules ==
* [[{{FULLPAGENAME}}/SimpleFilters|Simple Filters]]
* [[{{FULLPAGENAME}}/Editor|Editor]]

== Tutorials testing ==
* [[{{FULLPAGENAME}}/TutorialTesting/4.3-Release|4.3 Release]]

== Debug ==
* [[{{FULLPAGENAME}}/BRAINS_and_ITKv4_issue|BRAINS and ITKv4 issue]]

== Internals ==
* [[{{FULLPAGENAME}}/I18N|Internationalization]]
* [[{{FULLPAGENAME}}/Units|Units]]
* [https://github.com/TubeTK/SlicerExecutionModel/wiki/SlicerExecutionModel-Parameter-Serialization SlicerExecutionModel Parameter Serialization]

Documentation/4.3/Announcements

2013-09-13T16:27:14Z

Alexy: /* Other Improvements, Additions & Documentation */

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

{|width="100%"
|align="center"|
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]
|}

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Summary|Summary ]]
|[[#What is 3D Slicer|What is 3D Slicer]]
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]
|[[#Slicer Extensions|Slicer Extensions]]
|[[#Other Improvements, Additions & Documentation| Other Improvements, Additions & Documentation]]
|}
=Summary=

The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.

*Slicer {{documentation/version}} introduces
** a new App store, called the extension manager, for adding capabilities to Slicer. Close to 40 plug-ins are currently available.
** close to 500 feature improvements and bug fixes lead to improved performance and stability.
** augmentation of many modules.
** improved workflows in registration and dMRI
** the multivolume explorer allows interaction with time series and DCE data.
** major improvements to the DICOM module
** a new Markups module to streamline the use of fiducial lists

*Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker.
*Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.
*The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of courses for learning how to use Slicer. The portfolio contains self-guided presentation and sample data sets.

The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep the pages organized and up to date.

Find out more about Slicer {{documentation/version}} in the webinar held on [...]:

[[Image:Webinar-Slicer-4.1.png|link=http://vimeo.com/41096643|400px|center]]

=What is 3D Slicer=
Slicer is a community platform created for the purpose of subject specific image analysis and visualization.

* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* Multi organ from head to toe
* Bidirectional interface for devices
* Expandable and interfaced to multiple toolkits

There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]

=Slicer {{documentation/version}} Highlights=
<gallery caption="New and Improved Toolkits and Modules" widths="250px" heights="150px" perrow="3">
Image:ITK_logo.png|Moved from ITKv3 to ITKv4
Image:SimpleITK_Logo.png|Added SimpleITK
Image:CLIAutoRun.png|Added AutoRun mode for CLI modules to interactively search in parameter space and to create pipelines of filters. Watch the [https://vimeo.com/64813350 demo]!
Image:Markups-GUI-Collapsed.png|The [[Documentation/{{documentation/version}}/Modules/Markups|Markups]] module replaces Annotation fiducials.
</gallery>

= Slicer Extensions =

<gallery caption="New and Improved Extensions" widths="250px" heights="150px" perrow="4">
Image:AirwaySegmentation-ICON.png|[[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Airway Segmentation]] to segment the airway from chest CT images.{{new}}
Image:CMRTK-logo.png|[[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] to analyze cardiac LGE-MRI images. {{new}}
Image:ChangeTracker logo.png|[[Documentation/{{documentation/version}}/Extensions/ChangeTracker| Change Tracker]] for quantification of the subtle changes in pathology.{{new}}
Image:DiceSimilarityCoefficient.png|[[Documentation/{{documentation/version}}/Extensions/DiceComputation|Dice Computation]] to calculate the Dice Similarity Coefficient (DSC) between multiple label map images.{{new}}
Image:DTIAtlasBuilder.jpeg|[[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTI Atlas Builder]] to create an Atlas image as an average of several DTI images that will be registered.{{updated}}
Image:DTIPrep.png|[[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTI Prep]].{{updated}}
Image:DTIProcess-mj.png|[[Documentation/{{documentation/version}}/Extensions/DTIProcess| DTI Process]].{{updated}}
Image:ErodeDilateLabelIcon.png|[[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|Erode/Dilate Label]] to perform binary erosion and dilation on a specified label.{{new}}
Image:FacetedVisualizer.png|[[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|Faceted Visualizer]] to create flexible visualizations using Slicer by combining a 3D digital atlas and 3D scene models with an ontology.{{updated}}
Image:FiberViewerLight.png|[[Documentation/{{documentation/version}}/Extensions/FiberViewerLight| Fiber Viewer Light]] to create fiber clusters based on methods such as Length, Gravity, Hausdorff, or Mean Distribution and Normalized Cut.{{updated}}
Image:IASEM.png|[[Documentation/{{documentation/version}}/Extensions/IASEM| IASEM]] to segmentation and process of IASEM Electron Microscopy images.{{new}}
Image:QuickToolsLogo.png|[[Documentation/{{documentation/version}}/Extensions/ImageMaker|Image Maker]] to create volumes from scratch. {{new}}
Image:LAScarSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LAScarSegmenter|LA Scar Segmenter]] to perform segmentation of the left atrial scarring tissue from MR images. {{new}}
Image:LASegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LASegmenter|LA Segmenter]] to perform segmentation of the left atrium from MR images.{{new}}
Image:LongitudinalPETCTLogo.png|[[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT| Longitudinal PET/CT]] to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data.{{updated}
Image:MatlabBridgeLogo.png|[[Documentation/{{documentation/version}}/Extensions/MatlabBridge| Matlab Bridge]] to allow running Matlab functions directly in 3D Slicer.{{new}}
Image:ModelClipIcon.png|[[Documentation/{{documentation/version}}/Extensions/ModelClip| Model Clip]] to set osteotomy trajectory with multiple planes, and clip the model with just one click.{{new}}
Image:PathPlannerIcon.png|[[Documentation/{{documentation/version}}/Extensions/PathPlanner| Path Planner]]to facilitate the creation of trajectory.{{new}}
Image:PkModeling.png|[[Documentation/{{documentation/version}}/Extensions/PkModeling| Pk Modeling]] to calculate quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images.{{new}}
Image:PlusRemoteLogo.png|[[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] to send commands through OpenIGTLink Remote to PLUS.{{new}}
Image:Portplacement_icon.png|[[Documentation/{{documentation/version}}/Extensions/PortPlacement| Port Placement]]to assists in the planning of surgical port placement in laparoscopic procedures.{{new}}
Image:ReportingLogo.png|[[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] to create image annotations/markup that are stored in a structured form.{{updated}}
Image:SkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SkullStripper|Skull Stripper]] to register an atlas image to the patient data.{{updated}}
Image:SlicerIGTLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] to use all the advanced features of 3D Slicer for real-time navigation.{{new}}
Image:SlicerRT Logo 2.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] is a tool for powerful radiotherapy research. {{updated}}
Image:SlicerToKiwiExporterLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] to provide an easy way to export [[Documentation/{{documentation/version}}/Modules/Models|models]] into a [http://www.kiwiviewer.org/ KiwiViewer].{{new}}
Image:SobolevSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|Sobolev Segmenter]] implements Sobolev inner product based active contour, using the Chan-Vese energy functional.{{updated}}
Image:SwissSkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|Swiss Skull Stripper]] to register an atlas image to the patient data.{{new}}
Image:TrackerStabilizer.png|[[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Tracker Stabilizer]] to output a filtered transform node based on an tracker input (transform node).{{new}}
Image:TransformVisualizerLogo.png|[[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] to visualize any transform (linear transform, B-spline deformable transform, any other non-linear transform) or vector volume.{{new}}
Image:TubeTK-scaled.png|[[Documentation/{{documentation/version}}/Extensions/TubeTK| TubeTK]] is an open-source toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.{{updated}}
Image:UKFTractography.png|[[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKF Tractography]] a framework which uses an unscented Kalman filter for performing tractography.{{updated}}
Image:VisuaLine.png|[[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] to display lines in Slicer.{{updated}}
Image:WindowLevelEffectLogo.png|[[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|Window/Level Effect]] to adjust window/level for volumes using mouse and/or region of interest.{{new}}
Image:XNATSlicerIcon.jpg|[[Documentation/{{documentation/version}}/Extensions/XNATSlicer| XNAT Slicer]] Secure GUI-based IO with any XNAT server.{{new}}
Image:PerkTutorLogo.png|[[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] for training in image-guided needle interventions.{{new}}

<!-- You could user either {{new}} or {{updated}} macros.

</gallery>

= Other Improvements, Additions & Documentation =
<gallery caption="" widths="250px" heights="150px" perrow="3">
Image:SlicerModels-Large.svg|Added advanced controls for the [[Documentation/{{documentation/version}}/Modules/Models|model display representation]]
Image:SlicerModels-Large.svg|Depth peeling option for translucent surface models in [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D views]]

Image:Fiber select.PNG|Added [[Documentation/{{documentation/version}}/Modules/FiberBundleLabelSelect|fiber selection based on label map module]]

Image:TractographyDisplayModule.PNG|Added individual fiber editing option in [[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display module]]

Image:SlicerVolume-Large.svg|Added read/write support for [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|MRC files]]
Image:ctkDoubleSpinBox.gif|Improved support for image precision.
Image:QSlicerDarkStyle.png|Slicer theme for low intensity environment.
</gallery>

= For Developers: Looking at the Code Changes =

From a git checkout you can easily see the all the commits since the time of the 4.4.2 release:

git log --since="Sat Dec 8 03:32:53 2012"

To see a summary of your own commits, you could use something like:

git log --since="Sat Dec 8 03:32:53 2012" --oneline --author=pieper

see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.

[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]

= Related Projects =
<gallery caption="" widths="250px" heights="150px" perrow="3">
</gallery>

Documentation/4.3/Modules/TractographyDisplay

2013-09-13T16:26:00Z

Alexy:

Documentation/4.3/Modules/TractographyDisplay

2013-09-13T16:11:30Z

Alexy:

Documentation/4.3/Modules/TractographyDisplay

2013-09-13T16:09:54Z

Alexy:

File:TractographyDisplayModule.PNG

2013-09-13T16:08:46Z

Alexy: TractographyDisplayModule

TractographyDisplayModule

Documentation/4.3/Announcements

2013-09-13T15:43:17Z

Alexy: /* Other Improvements, Additions & Documentation */

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

{|width="100%"
|align="center"|
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]
|}

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Summary|Summary ]]
|[[#What is 3D Slicer|What is 3D Slicer]]
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]
|[[#Slicer Extensions|Slicer Extensions]]
|[[#Other Improvements, Additions & Documentation| Other Improvements, Additions & Documentation]]
|}
=Summary=

The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.

*Slicer {{documentation/version}} introduces
** a new App store, called the extension manager, for adding capabilities to Slicer. Close to 40 plug-ins are currently available.
** close to 500 feature improvements and bug fixes lead to improved performance and stability.
** augmentation of many modules.
** improved workflows in registration and dMRI
** the multivolume explorer allows interaction with time series and DCE data.
** major improvements to the DICOM module
** a new Markups module to streamline the use of fiducial lists

*Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker.
*Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.
*The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of courses for learning how to use Slicer. The portfolio contains self-guided presentation and sample data sets.

The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep the pages organized and up to date.

Find out more about Slicer {{documentation/version}} in the webinar held on [...]:

[[Image:Webinar-Slicer-4.1.png|link=http://vimeo.com/41096643|400px|center]]

=What is 3D Slicer=
Slicer is a community platform created for the purpose of subject specific image analysis and visualization.

* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* Multi organ from head to toe
* Bidirectional interface for devices
* Expandable and interfaced to multiple toolkits

There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]

=Slicer {{documentation/version}} Highlights=
<gallery caption="New and Improved Toolkits and Modules" widths="250px" heights="150px" perrow="3">
Image:ITK_logo.png|Moved from ITKv3 to ITKv4
Image:SimpleITK_Logo.png|Added SimpleITK
Image:CLIAutoRun.png|Added AutoRun mode for CLI modules to interactively search in parameter space and to create pipelines of filters. Watch the [https://vimeo.com/64813350 demo]!
Image:Markups-GUI-Collapsed.png|The [[Documentation/{{documentation/version}}/Modules/Markups|Markups]] module replaces Annotation fiducials.
</gallery>

= Slicer Extensions =

<gallery caption="New and Improved Extensions" widths="250px" heights="150px" perrow="4">
Image:AirwaySegmentation-ICON.png|[[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Airway Segmentation]] to segment the airway from chest CT images.{{new}}
Image:CMRTK-logo.png|[[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] to analyze cardiac LGE-MRI images. {{new}}
Image:ChangeTracker logo.png|[[Documentation/{{documentation/version}}/Extensions/ChangeTracker| Change Tracker]] for quantification of the subtle changes in pathology.{{new}}
Image:DiceSimilarityCoefficient.png|[[Documentation/{{documentation/version}}/Extensions/DiceComputation|Dice Computation]] to calculate the Dice Similarity Coefficient (DSC) between multiple label map images.{{new}}
Image:DTIAtlasBuilder.jpeg|[[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTI Atlas Builder]] to create an Atlas image as an average of several DTI images that will be registered.{{updated}}
Image:DTIPrep.png|[[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTI Prep]].{{updated}}
Image:DTIProcess-mj.png|[[Documentation/{{documentation/version}}/Extensions/DTIProcess| DTI Process]].{{updated}}
Image:ErodeDilateLabelIcon.png|[[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|Erode/Dilate Label]] to perform binary erosion and dilation on a specified label.{{new}}
Image:FacetedVisualizer.png|[[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|Faceted Visualizer]] to create flexible visualizations using Slicer by combining a 3D digital atlas and 3D scene models with an ontology.{{updated}}
Image:FiberViewerLight.png|[[Documentation/{{documentation/version}}/Extensions/FiberViewerLight| Fiber Viewer Light]] to create fiber clusters based on methods such as Length, Gravity, Hausdorff, or Mean Distribution and Normalized Cut.{{updated}}
Image:IASEM.png|[[Documentation/{{documentation/version}}/Extensions/IASEM| IASEM]] to segmentation and process of IASEM Electron Microscopy images.{{new}}
Image:QuickToolsLogo.png|[[Documentation/{{documentation/version}}/Extensions/ImageMaker|Image Maker]] to create volumes from scratch. {{new}}
Image:LAScarSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LAScarSegmenter|LA Scar Segmenter]] to perform segmentation of the left atrial scarring tissue from MR images. {{new}}
Image:LASegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LASegmenter|LA Segmenter]] to perform segmentation of the left atrium from MR images.{{new}}
Image:LongitudinalPETCTLogo.png|[[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT| Longitudinal PET/CT]] to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data.{{updated}
Image:MatlabBridgeLogo.png|[[Documentation/{{documentation/version}}/Extensions/MatlabBridge| Matlab Bridge]] to allow running Matlab functions directly in 3D Slicer.{{new}}
Image:ModelClipIcon.png|[[Documentation/{{documentation/version}}/Extensions/ModelClip| Model Clip]] to set osteotomy trajectory with multiple planes, and clip the model with just one click.{{new}}
Image:PathPlannerIcon.png|[[Documentation/{{documentation/version}}/Extensions/PathPlanner| Path Planner]]to facilitate the creation of trajectory.{{new}}
Image:PkModeling.png|[[Documentation/{{documentation/version}}/Extensions/PkModeling| Pk Modeling]] to calculate quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images.{{new}}
Image:PlusRemoteLogo.png|[[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] to send commands through OpenIGTLink Remote to PLUS.{{new}}
Image:Portplacement_icon.png|[[Documentation/{{documentation/version}}/Extensions/PortPlacement| Port Placement]]to assists in the planning of surgical port placement in laparoscopic procedures.{{new}}
Image:ReportingLogo.png|[[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] to create image annotations/markup that are stored in a structured form.{{updated}}
Image:SkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SkullStripper|Skull Stripper]] to register an atlas image to the patient data.{{updated}}
Image:SlicerIGTLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] to use all the advanced features of 3D Slicer for real-time navigation.{{new}}
Image:SlicerRT Logo 2.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] is a tool for powerful radiotherapy research. {{updated}}
Image:SlicerToKiwiExporterLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] to provide an easy way to export [[Documentation/{{documentation/version}}/Modules/Models|models]] into a [http://www.kiwiviewer.org/ KiwiViewer].{{new}}
Image:SobolevSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|Sobolev Segmenter]] implements Sobolev inner product based active contour, using the Chan-Vese energy functional.{{updated}}
Image:SwissSkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|Swiss Skull Stripper]] to register an atlas image to the patient data.{{new}}
Image:TrackerStabilizer.png|[[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Tracker Stabilizer]] to output a filtered transform node based on an tracker input (transform node).{{new}}
Image:TransformVisualizerLogo.png|[[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] to visualize any transform (linear transform, B-spline deformable transform, any other non-linear transform) or vector volume.{{new}}
Image:TubeTK-scaled.png|[[Documentation/{{documentation/version}}/Extensions/TubeTK| TubeTK]] is an open-source toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.{{updated}}
Image:UKFTractography.png|[[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKF Tractography]] a framework which uses an unscented Kalman filter for performing tractography.{{updated}}
Image:VisuaLine.png|[[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] to display lines in Slicer.{{updated}}
Image:WindowLevelEffectLogo.png|[[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|Window/Level Effect]] to adjust window/level for volumes using mouse and/or region of interest.{{new}}
Image:XNATSlicerIcon.jpg|[[Documentation/{{documentation/version}}/Extensions/XNATSlicer| XNAT Slicer]] Secure GUI-based IO with any XNAT server.{{new}}

<!-- You could user either {{new}} or {{updated}} macros.

</gallery>

= Other Improvements, Additions & Documentation =
<gallery caption="" widths="250px" heights="150px" perrow="3">
Image:SlicerModels-Large.svg|Added advanced controls for the [[Documentation/{{documentation/version}}/Modules/Models|model display representation]]
Image:SlicerModels-Large.svg|Depth peeling option for translucent surface models in [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D views]]

Image:Fiber select.PNG|Added [[Documentation/{{documentation/version}}/Modules/FiberBundleLabelSelect|fiber selection based on label map module]]

Image:Fiber select.PNG|Added individual fiber editing option in [[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display module]]

Image:SlicerVolume-Large.svg|Added read/write support for [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|MRC files]]
Image:ctkDoubleSpinBox.gif|Improved support for image precision.
Image:QSlicerDarkStyle.png|Slicer theme for low intensity environment.
</gallery>

= For Developers: Looking at the Code Changes =

From a git checkout you can easily see the all the commits since the time of the 4.4.2 release:

git log --since="Sat Dec 8 03:32:53 2012"

To see a summary of your own commits, you could use something like:

git log --since="Sat Dec 8 03:32:53 2012" --oneline --author=pieper

see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.

[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]

= Related Projects =
<gallery caption="" widths="250px" heights="150px" perrow="3">
</gallery>

Documentation/4.3/Announcements

2013-09-13T15:41:39Z

Alexy: /* Other Improvements, Additions & Documentation */

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

{|width="100%"
|align="center"|
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]
|}

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Summary|Summary ]]
|[[#What is 3D Slicer|What is 3D Slicer]]
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]
|[[#Slicer Extensions|Slicer Extensions]]
|[[#Other Improvements, Additions & Documentation| Other Improvements, Additions & Documentation]]
|}
=Summary=

The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.

*Slicer {{documentation/version}} introduces
** a new App store, called the extension manager, for adding capabilities to Slicer. Close to 40 plug-ins are currently available.
** close to 500 feature improvements and bug fixes lead to improved performance and stability.
** augmentation of many modules.
** improved workflows in registration and dMRI
** the multivolume explorer allows interaction with time series and DCE data.
** major improvements to the DICOM module
** a new Markups module to streamline the use of fiducial lists

*Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker.
*Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.
*The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of courses for learning how to use Slicer. The portfolio contains self-guided presentation and sample data sets.

The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep the pages organized and up to date.

Find out more about Slicer {{documentation/version}} in the webinar held on [...]:

[[Image:Webinar-Slicer-4.1.png|link=http://vimeo.com/41096643|400px|center]]

=What is 3D Slicer=
Slicer is a community platform created for the purpose of subject specific image analysis and visualization.

* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy
* Multi organ from head to toe
* Bidirectional interface for devices
* Expandable and interfaced to multiple toolkits

There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]

=Slicer {{documentation/version}} Highlights=
<gallery caption="New and Improved Toolkits and Modules" widths="250px" heights="150px" perrow="3">
Image:ITK_logo.png|Moved from ITKv3 to ITKv4
Image:SimpleITK_Logo.png|Added SimpleITK
Image:CLIAutoRun.png|Added AutoRun mode for CLI modules to interactively search in parameter space and to create pipelines of filters. Watch the [https://vimeo.com/64813350 demo]!
Image:Markups-GUI-Collapsed.png|The [[Documentation/{{documentation/version}}/Modules/Markups|Markups]] module replaces Annotation fiducials.
</gallery>

= Slicer Extensions =

<gallery caption="New and Improved Extensions" widths="250px" heights="150px" perrow="4">
Image:AirwaySegmentation-ICON.png|[[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Airway Segmentation]] to segment the airway from chest CT images.{{new}}
Image:CMRTK-logo.png|[[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] to analyze cardiac LGE-MRI images. {{new}}
Image:ChangeTracker logo.png|[[Documentation/{{documentation/version}}/Extensions/ChangeTracker| Change Tracker]] for quantification of the subtle changes in pathology.{{new}}
Image:DiceSimilarityCoefficient.png|[[Documentation/{{documentation/version}}/Extensions/DiceComputation|Dice Computation]] to calculate the Dice Similarity Coefficient (DSC) between multiple label map images.{{new}}
Image:DTIAtlasBuilder.jpeg|[[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTI Atlas Builder]] to create an Atlas image as an average of several DTI images that will be registered.{{updated}}
Image:DTIPrep.png|[[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTI Prep]].{{updated}}
Image:DTIProcess-mj.png|[[Documentation/{{documentation/version}}/Extensions/DTIProcess| DTI Process]].{{updated}}
Image:ErodeDilateLabelIcon.png|[[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|Erode/Dilate Label]] to perform binary erosion and dilation on a specified label.{{new}}
Image:FacetedVisualizer.png|[[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|Faceted Visualizer]] to create flexible visualizations using Slicer by combining a 3D digital atlas and 3D scene models with an ontology.{{updated}}
Image:FiberViewerLight.png|[[Documentation/{{documentation/version}}/Extensions/FiberViewerLight| Fiber Viewer Light]] to create fiber clusters based on methods such as Length, Gravity, Hausdorff, or Mean Distribution and Normalized Cut.{{updated}}
Image:IASEM.png|[[Documentation/{{documentation/version}}/Extensions/IASEM| IASEM]] to segmentation and process of IASEM Electron Microscopy images.{{new}}
Image:QuickToolsLogo.png|[[Documentation/{{documentation/version}}/Extensions/ImageMaker|Image Maker]] to create volumes from scratch. {{new}}
Image:LAScarSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LAScarSegmenter|LA Scar Segmenter]] to perform segmentation of the left atrial scarring tissue from MR images. {{new}}
Image:LASegmenter.png|[[Documentation/{{documentation/version}}/Extensions/LASegmenter|LA Segmenter]] to perform segmentation of the left atrium from MR images.{{new}}
Image:LongitudinalPETCTLogo.png|[[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT| Longitudinal PET/CT]] to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data.{{updated}
Image:MatlabBridgeLogo.png|[[Documentation/{{documentation/version}}/Extensions/MatlabBridge| Matlab Bridge]] to allow running Matlab functions directly in 3D Slicer.{{new}}
Image:ModelClipIcon.png|[[Documentation/{{documentation/version}}/Extensions/ModelClip| Model Clip]] to set osteotomy trajectory with multiple planes, and clip the model with just one click.{{new}}
Image:PathPlannerIcon.png|[[Documentation/{{documentation/version}}/Extensions/PathPlanner| Path Planner]]to facilitate the creation of trajectory.{{new}}
Image:PkModeling.png|[[Documentation/{{documentation/version}}/Extensions/PkModeling| Pk Modeling]] to calculate quantitative parameters from Dynamic Contrast Enhanced DCE-MRI images.{{new}}
Image:PlusRemoteLogo.png|[[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] to send commands through OpenIGTLink Remote to PLUS.{{new}}
Image:Portplacement_icon.png|[[Documentation/{{documentation/version}}/Extensions/PortPlacement| Port Placement]]to assists in the planning of surgical port placement in laparoscopic procedures.{{new}}
Image:ReportingLogo.png|[[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] to create image annotations/markup that are stored in a structured form.{{updated}}
Image:SkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SkullStripper|Skull Stripper]] to register an atlas image to the patient data.{{updated}}
Image:SlicerIGTLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] to use all the advanced features of 3D Slicer for real-time navigation.{{new}}
Image:SlicerRT Logo 2.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] is a tool for powerful radiotherapy research. {{updated}}
Image:SlicerToKiwiExporterLogo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]] to provide an easy way to export [[Documentation/{{documentation/version}}/Modules/Models|models]] into a [http://www.kiwiviewer.org/ KiwiViewer].{{new}}
Image:SobolevSegmenter.png|[[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|Sobolev Segmenter]] implements Sobolev inner product based active contour, using the Chan-Vese energy functional.{{updated}}
Image:SwissSkullStripper.png|[[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|Swiss Skull Stripper]] to register an atlas image to the patient data.{{new}}
Image:TrackerStabilizer.png|[[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Tracker Stabilizer]] to output a filtered transform node based on an tracker input (transform node).{{new}}
Image:TransformVisualizerLogo.png|[[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] to visualize any transform (linear transform, B-spline deformable transform, any other non-linear transform) or vector volume.{{new}}
Image:TubeTK-scaled.png|[[Documentation/{{documentation/version}}/Extensions/TubeTK| TubeTK]] is an open-source toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.{{updated}}
Image:UKFTractography.png|[[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKF Tractography]] a framework which uses an unscented Kalman filter for performing tractography.{{updated}}
Image:VisuaLine.png|[[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] to display lines in Slicer.{{updated}}
Image:WindowLevelEffectLogo.png|[[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|Window/Level Effect]] to adjust window/level for volumes using mouse and/or region of interest.{{new}}
Image:XNATSlicerIcon.jpg|[[Documentation/{{documentation/version}}/Extensions/XNATSlicer| XNAT Slicer]] Secure GUI-based IO with any XNAT server.{{new}}

<!-- You could user either {{new}} or {{updated}} macros.

</gallery>

= Other Improvements, Additions & Documentation =
<gallery caption="" widths="250px" heights="150px" perrow="3">
Image:SlicerModels-Large.svg|Added advanced controls for the [[Documentation/{{documentation/version}}/Modules/Models|model display representation]]
Image:SlicerModels-Large.svg|Depth peeling option for translucent surface models in [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D views]]

Image:fiber_select.png|Added [[Documentation/{{documentation/version}}/Modules/FiberBundleLabelSelect|fiber selection based on label map module]]

Image:fiber_select.png|Added individual fiber editing option in [[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display module]]

Image:SlicerVolume-Large.svg|Added read/write support for [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|MRC files]]
Image:ctkDoubleSpinBox.gif|Improved support for image precision.
Image:QSlicerDarkStyle.png|Slicer theme for low intensity environment.
</gallery>

= For Developers: Looking at the Code Changes =

From a git checkout you can easily see the all the commits since the time of the 4.4.2 release:

git log --since="Sat Dec 8 03:32:53 2012"

To see a summary of your own commits, you could use something like:

git log --since="Sat Dec 8 03:32:53 2012" --oneline --author=pieper

see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.

[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]

= Related Projects =
<gallery caption="" widths="250px" heights="150px" perrow="3">
</gallery>

Documentation/4.3/Modules/FiberBundleLabelSelect

2013-09-13T15:33:52Z

Alexy:

Documentation/4.3/Modules/FiberBundleLabelSelect

2013-09-13T15:32:54Z

Alexy:

Documentation/4.3/Modules/FiberBundleLabelSelect

2013-09-13T15:29:25Z

Alexy:

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Alex Yarmarkovich, Isomics, SPL 
Contributor1: Demian Wassermann, SPL 
Contact: Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module is used for selecting a subset of DTI fiber tracts including or excluding certain fibers passing through a selected set of labels in the label map volume.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1: Filter out a subset of DTI fiber tracts which are passing through selected region(s) defined in the label map volume.
* Use Case 2: Filter out a subset of DTI fiber tracts which are NOT passing through selected region(s) defined in the label map volume.
* Use Case 3: A combination of Case 1 and Case 2.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial Slicer 4 Diffusion Tensor Tutorial]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
* Parameters panel:
** Parameters: select an existing setting for the module or create a new one.
* IO panel:
** Input Label Map: select an existing label map volume.
** Input FiberBundle: Select the fibers that you want to filter.
** Output FiberBundle: Select the bundle that you want to create or modify from a list.
* Label Regions Definition panel :
** Labels to include: A comma separated list of label values to include in the output fiber bundles set.
** Fiducail Seeding Step Size: Step between the seeding samples in the box (mm).
** Seed Selected Fiducials: Flag indicating whether to use only selected fiducials for seeding or all of them.
** Maximum Number of Seeds: Used with models to specify the limit of the number of vertices to be used for seeding.
| align="right" |
[[Image:Fiber select.PNG|thumb|280px|FiberBundleLabelSelect]]
|-
|
* Label Map Options panel:
** Use Index Space: if selected seed at IJK voxel grid
** Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off.
** Random Grid: use random placement.
** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
** ROI Labels: a comma separated list of label to start seeding
** Write Fibers to Disk: option to save the results to disk for further analysis.
** Output Directory: path where the results are saved.
** File Prefix Name: name that would be used for each output bundle.
| align="right" |
[[Image:Tractography_LabelMap_Seeding.PNG|thumb|280px|Label Map Tractography Seeding]]
|}

* Tractography Seeding Parameters panel:
** Minimum Path Length: Select only tracts that are longer than this value (mm).
** Maximum Path Length: Select only tracts that are shorter than this value (mm).
** Stopping Criteria: Select Linear Measure or FA to be used as stopping criteria.
** Stopping Value: Select Linear Measure or FA stopping value, tracking will stop when the value drops below this one.
** Stopping Track Curvature: Select the curvature stopping value in degree per mm, tracking will stop when the radius of curvature is smaller than this one.

* Enabling Options panel:
** Create Tracts Initially As: Select Tubes or Lines


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Tractography Label Map Seeding


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

File:Fiber select.PNG

2013-09-13T15:27:38Z

Alexy: FiberBundleLableSelect module

FiberBundleLableSelect module

Documentation/4.3/Modules/FiberBundleLabelSelect

2013-09-13T15:26:08Z

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

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Alex Yarmarkovich, Isomics, SPL 
Contributor1: Demian Wassermann, SPL 
Contact: Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
This module is used for selecting a subset of DTI fiber tracts including or excluding certain fibers passing through a selected set of labels in the label map volume.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1: Filter out a subset of DTI fiber tracts which are passing through selected region(s) defined in the label map volume.
* Use Case 2: Filter out a subset of DTI fiber tracts which are NOT passing through selected region(s) defined in the label map volume.
* Use Case 3: A combination of Case 1 and Case 2.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial Slicer 4 Diffusion Tensor Tutorial]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
* Parameters panel:
** Parameters: select an existing setting for the module or create a new one.
* IO panel:
** Input Label Map: select an existing label map volume.
** Input FiberBundle: Select the fibers that you want to filter.
** Output FiberBundle: Select the bundle that you want to create or modify from a list.
* Label Regions Definition panel :
** Labels to include: A comma separated list of label values to include in the output fiber bundles set.
** Fiducail Seeding Step Size: Step between the seeding samples in the box (mm).
** Seed Selected Fiducials: Flag indicating whether to use only selected fiducials for seeding or all of them.
** Maximum Number of Seeds: Used with models to specify the limit of the number of vertices to be used for seeding.
| align="right" |
[[Image:Tractography_Fiducial_Seeding.PNG|thumb|280px|Fiducial Tractography Seeding]]
|-
|
* Label Map Options panel:
** Use Index Space: if selected seed at IJK voxel grid
** Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off.
** Random Grid: use random placement.
** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
** ROI Labels: a comma separated list of label to start seeding
** Write Fibers to Disk: option to save the results to disk for further analysis.
** Output Directory: path where the results are saved.
** File Prefix Name: name that would be used for each output bundle.
| align="right" |
[[Image:Tractography_LabelMap_Seeding.PNG|thumb|280px|Label Map Tractography Seeding]]
|}

* Tractography Seeding Parameters panel:
** Minimum Path Length: Select only tracts that are longer than this value (mm).
** Maximum Path Length: Select only tracts that are shorter than this value (mm).
** Stopping Criteria: Select Linear Measure or FA to be used as stopping criteria.
** Stopping Value: Select Linear Measure or FA stopping value, tracking will stop when the value drops below this one.
** Stopping Track Curvature: Select the curvature stopping value in degree per mm, tracking will stop when the radius of curvature is smaller than this one.

* Enabling Options panel:
** Create Tracts Initially As: Select Tubes or Lines


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Tractography Label Map Seeding


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.3/Modules

2013-09-13T15:14:08Z

Alexy: /* Diffusion */

<noinclude>{{documentation/versioncheck}}</noinclude>
=Modules by Category=
==Core Modules==

{{documentation/{{documentation/version}}/Developers/random-image}}

*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
**[[Documentation/{{documentation/version}}/Modules/Editor/WatershedFromMarkers|WatershedFromMarkers]] (Bradley Lowekamp) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Markups|Markups]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)

==Wizards==

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) {{wip}}
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)
**[[Documentation/{{documentation/version}}/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao) {{wip}}

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*[[Documentation/{{documentation/version}}/Modules/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)
**[[Documentation/{{documentation/version}}/Modules/LAScarSegmenter|Left Atrial Scar Segmenter]] (LiangJia Zhu) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (LiangJia Zhu) {{wip}}
==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/SNR Measurement|SNR Measurement]] (Babak Matinfar)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) {{wip}}
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Interactive Seeding]] (Alex Yarmarkovich)
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/FiberBundleLabelSelect|FiberBundleLabelSelect]] (Alex Yarmarkovich) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) {{wip}}
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/FiberBundleToLabelMap|Fiber Bundle to Label Map]] (Steve Pieper)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) {{wip}}

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/SimpleFilters|Simple Filters]] (Bradley Lowekamp) {{wip}}
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) {{wip}}
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) {{wip}}

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] {{wip}}
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/SurfaceToolbox| SurfaceToolbox]] (Luca Antiga)

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)
{{wip}}

==Endoscopy==
*[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

=={{wip}} Work in Progress {{wip}}==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) {{wip}}
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett){{wip}}

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) {{wip}}

Documentation/Nightly/Modules

2013-08-13T21:45:03Z

Alexy: /* Diffusion */

<noinclude>{{documentation/versioncheck}}</noinclude>
=Modules by Category=
==Core Modules==

{{documentation/{{documentation/version}}/Developers/random-image}}

*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
**[[Documentation/{{documentation/version}}/Modules/Editor/WatershedFromMarkers|WatershedFromMarkers]] (Bradley Lowekamp) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)

==Wizards==

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) {{wip}}
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)
**[[Documentation/{{documentation/version}}/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao) {{wip}}

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*[[Documentation/{{documentation/version}}/Modules/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)
**[[Documentation/{{documentation/version}}/Modules/LAScarSegmenter|Left Atrial Scar Segmenter]] (LiangJia Zhu) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (LiangJia Zhu) {{wip}}
==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/SNR Measurement|SNR Measurement]] (Babak Matinfar)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) {{wip}}
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Interactive Seeding]] (Alex Yarmarkovich)
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) {{wip}}
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/FiberBundleToLabelMap|Fiber Bundle to Label Map]] (Steve Pieper)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) {{wip}}

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/SimpleFilters|Simple Filters]] (Bradley Lowekamp) {{wip}}
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) {{wip}}
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) {{wip}}

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] {{wip}}
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) {{wip}}

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)
{{wip}}

==Endoscopy==
*[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

=={{wip}} Work in Progress {{wip}}==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) {{wip}}
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett){{wip}}

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) {{wip}}

Documentation/Nightly/Modules

2013-08-13T21:44:08Z

Alexy: /* Diffusion */

<noinclude>{{documentation/versioncheck}}</noinclude>
=Modules by Category=
==Core Modules==

{{documentation/{{documentation/version}}/Developers/random-image}}

*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
**[[Documentation/{{documentation/version}}/Modules/Editor/WatershedFromMarkers|WatershedFromMarkers]] (Bradley Lowekamp) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)

==Wizards==

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) {{wip}}
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)
**[[Documentation/{{documentation/version}}/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao) {{wip}}

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*[[Documentation/{{documentation/version}}/Modules/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)
**[[Documentation/{{documentation/version}}/Modules/LAScarSegmenter|Left Atrial Scar Segmenter]] (LiangJia Zhu) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (LiangJia Zhu) {{wip}}
==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/SNR Measurement|SNR Measurement]] (Babak Matinfar)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) {{wip}}
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Interactive Seeding]] (Alex Yarmarkovich)
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) {{wip}}
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/FiberBundleToLabelMap|Fiber Bundle to Label Map]] (Steve Pieper)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) {{wip}}

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/SimpleFilters|Simple Filters]] (Bradley Lowekamp) {{wip}}
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) {{wip}}
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) {{wip}}

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] {{wip}}
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) {{wip}}

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)
{{wip}}

==Endoscopy==
*[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

=={{wip}} Work in Progress {{wip}}==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) {{wip}}
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett){{wip}}

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) {{wip}}

Documentation/Nightly/Modules

2013-08-13T21:43:17Z

Alexy: /* Diffusion */

<noinclude>{{documentation/versioncheck}}</noinclude>
=Modules by Category=
==Core Modules==

{{documentation/{{documentation/version}}/Developers/random-image}}

*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
**[[Documentation/{{documentation/version}}/Modules/Editor/WatershedFromMarkers|WatershedFromMarkers]] (Bradley Lowekamp) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)

==Wizards==

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) {{wip}}
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)
**[[Documentation/{{documentation/version}}/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao) {{wip}}

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*[[Documentation/{{documentation/version}}/Modules/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)
**[[Documentation/{{documentation/version}}/Modules/LAScarSegmenter|Left Atrial Scar Segmenter]] (LiangJia Zhu) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (LiangJia Zhu) {{wip}}
==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/SNR Measurement|SNR Measurement]] (Babak Matinfar)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) {{wip}}
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Interactive Seeding]] (Alex Yarmarkovich) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) {{wip}}
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]] {{wip}} (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/FiberBundleToLabelMap|Fiber Bundle to Label Map]] (Steve Pieper)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) {{wip}}

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/SimpleFilters|Simple Filters]] (Bradley Lowekamp) {{wip}}
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) {{wip}}
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) {{wip}}
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) {{wip}}

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] {{wip}}
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) {{wip}}

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)
{{wip}}

==Endoscopy==
*[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

=={{wip}} Work in Progress {{wip}}==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) {{wip}}
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) {{wip}}
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) {{wip}}
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] {{wip}}
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett){{wip}}

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) {{wip}}