Slicer Wiki - User contributions [en]

Documentation/4.0/Developers/Build Instructions

2013-01-08T04:40:31Z

Pkarasev: /* Platform Notes */

{{mbox
| text = The goal of the [[{{tool|logo|cmake}}|x16px]] [{{tool|homepage|cmake}} CMake] '''Super-Build''' is to provide a cross-platform build system that allows developers to quickly install and configure the multiple packages. Where [[Slicer3:Build_Instructions|Slicer3's build system]] relied on a [[Slicer3:getbuildtest|custom build script called getbuildtest]], new features added to [{{tool|homepage|cmake}} CMake], partly driven by slicer's requirements, allow porting of the scripts to rely more on native [{{tool|homepage|cmake}} CMake] functionality with the benefit that build script is more modular and general purpose.
}}
 

== PREREQUISITES ==
 
<center>To avoid [[#Common_errors|'''Common errors''']], we '''STRONGLY''' recommend to read the [[Documentation/{{documentation/version}}/Developers/Build Instructions/Prerequisites|Prerequisites]] section.</center>

 

== CHECKOUT slicer source files ==

Two options: <code>svn</code> or <code>git-svn</code>

To make '''review''' and '''integration''' of your welcome contributions, we recommends the use of <code>git-svn</code>

 
{{ambox
| type = warning
| text = While it is not enforced, we strongly recommend you to '''AVOID''' the use of '''SPACES''' for both the <code>source directory</code> and the <code>build directory</code>. We mean it.
}}
 

Note that even if you use <code>svn</code> to check out Slicer source code, you will need to have <code>git</code> installed to checkout and build other libraries. '''YES''', you need to install the things listed in the [[Documentation/{{documentation/version}}/Developers/Build Instructions/Prerequisites|prerequisites]] !.

=== Using <code>git-svn</code> ===

git clone git://github.com/Slicer/Slicer.git
cd Slicer
git svn init http://svn.slicer.org/Slicer4/trunk
git update-ref refs/remotes/git-svn refs/remotes/origin/master
git checkout master
git svn rebase

Consider reading the following page: [[Slicer:git-svn|Slicer guide to <code>git-svn</code>]]

=== Using <code>svn</code> ===

cd MyProjects
svn co [http://svn.slicer.org/Slicer4/trunk http://svn.slicer.org/Slicer4/trunk] Slicer4

 

== CONFIGURE and generate Slicer solution files ==
You can configure and generate Slicer solution files using either <code>ccmake</code> or <code>cmake-gui</code>.
=== Per-platform instructions===
==== Windows ====
*'''Recommended''': <code>cmake-gui</code>
** Configure using default options.
* '''Remarks''':
#If you downloaded the Qt binary then <code>qmake</code> will be detected and all paths will be set automatically.
#If you built your own Qt (e.g. in Debug mode for use with the designer) set the <code>QT_QMAKE_EXECUTABLE</code> in <code>cmake-gui</code>.<code>QT_QMAKE_EXECUTABLE</code> should be set to the path of the qmake.exe file, which is inside the bin directory (for example, <code>/path/to/qt-everywhere-opensource-build-4.7.4/bin/qmake.exe</code>).
#Windows doesn't support path longer than 260 characters, please make sure that the total path name of your <code>Slicer-build</code> directory is no longer than 50 characters ( for example <code>c:\work\Slicer\Slicer-Superbuild</code> (32 characters) is fine)

==== Unix-like ====
*'''Recommended''': <code>ccmake</code>
** Configure using the following commands. By default '''CMAKE_BUILD_TYPE''' is set to '''Debug'''.
<pre>
mkdir Slicer4-SuperBuild-Debug
cd Slicer4-SuperBuild-Debug
ccmake -DQT_QMAKE_EXECUTABLE:FILEPATH=/path/to/QtSDK-1.2/Desktop/Qt/474/gcc/bin/qmake ../Slicer4
</pre>
* '''Remarks''':
# Using top-level directory name like <code>Slicer-Superbuild-Release</code> or <code>Slicer-Superbuild-Debug</code> is recommended.

=== General information ===

Two projects are generated by either <code>cmake</code>, <code>ccmake</code> or <code>cmake-gui</code>.

One of them is in the top-level bin directory <code>Slicer4-Superbuild</code> and the other one is in the subdirectory <code>Slicer-build</code>:

<pre>Slicer4-Superbuild/Slicer-build</pre>

# The first project in <code>Slicer4-Superbuild</code> manages all the external dependencies of Slicer (VTK, ITK, Python, ...). To build Slicer for the first time, run make (or build the solution file in Visual Studio) in <code>Slicer4-Superbuild</code>, which will update and build the external libraries and if successful will then build the subproject Slicer-build. 
# The second project in <code>Slicer4-Superbuild/Slicer-build</code> is the "traditional" build directory of Slicer. After local changes in Slicer (or after an svn update on the source directory of Slicer), only running make (or building the solution file in Visual Studio) in <code>Slicer4-Superbuild/Slicer-build</code> is necessary (the external libraries are considered built and up to date). 
#'''Warning''': An important amount of disk space is required to compile Slicer in Debug (>10GB on Windows)

=== Workaround firewall blocking git protocol ===
* Some firewall will be blocking the git protocol, a possible workaround is to configure Slicer disabling the option <code>Slicer_USE_GIT_PROTOCOL</code>. Then http protocol will be used instead. Consider also reading https://github.com/commontk/CTK/issues/33

=== Notes for advanced users ===
* By default, if CMake finds Java on your machine, it automatically builds Java CLIs. If you don't want any Java in your Slicer (or if you don't want to install Java on your Mac Os X), you can pass <code>-DCMAKE_DISABLE_FIND_PACKAGE_Java:BOOL=TRUE</code> when configuring Slicer.
* Same applies for OpenSSL: <code>CMAKE_DISABLE_FIND_PACKAGE_OpenSSL:BOOL=TRUE</code> can be passed when building Slicer for packaging.

 

== BUILD Slicer4 ==
After configuration, start the build process in the <code>Slicer4-SuperBuild</code> directory

=== Per-platform instructions===
==== Windows ====
* Open <code>Slicer4-SuperBuild\Slicer.sln</code> in Visual Studio
* Select your build configuration. Usually '''Release''' of '''Debug'''
* Build the <code>ALL_BUILD</code> project.

* If you make local changes to Slicer4, open the solution file located in the directory <code>Slicer4-SuperBuild/Slicer-build</code> instead. You should then be able to either build all projects or just a specific one.

==== Unix-like ====

cd ~/Projects/Slicer4-SuperBuild
make -j<NUMBEROFCORES>

 

== RUN Slicer ==
=== Per-platform instructions===
==== Windows ====

Run <code>Slicer4-SuperBuild/Slicer-build/Slicer.exe</code>

==== Unix-like ====

Run <code>Slicer4-SuperBuild/Slicer-build/Slicer</code>

 

== DEBUG Slicer ==
=== Per-platform instructions===
==== Windows ====
* Make sure you build Slicer using the '''Debug''' configuration.
* Open a windows terminal <code>cmd.exe</code>
* Execute the following command:
cd \path\to\Slicer4-SuperBuild\Slicer-build
Slicer.exe --VisualStudio Slicer.sln

==== Unix-like ====
NA

 

== Common errors ==
=== error: ‘class QList<QString>’ has no member named ‘reserve’ ===
/nfs/Users/blowekamp/QtSDK/Desktop/Qt/474/gcc/include/QtCore/qdatastream.h: In function ‘QDataStream& operator>>(QDataStream&, QList<T>&) [with T = QString]’:
/nfs/Users/blowekamp/QtSDK/Desktop/Qt/474/gcc/include/QtCore/qstringlist.h:247: instantiated from here
/nfs/Users/blowekamp/QtSDK/Desktop/Qt/474/gcc/include/QtCore/qdatastream.h:246: error: ‘class QList<QString>’ has no member named ‘reserve’
You have multiple Qt versions installed on your machine. Try removing the Qt version installed on the system.

=== libarchive.so: undefined reference to `SHA256_Update' ===

Linking CXX executable ../../../../../bin/MRMLLogicCxxTests
/home/benjaminlong/work/slicer/Slicer4-Superbuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `SHA256_Update'
/home/benjaminlong/work/slicer/Slicer4-Superbuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `SHA256_Final'
/home/benjaminlong/work/slicer/Slicer4-Superbuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `SHA256_Init'
/home/benjaminlong/work/slicer/Slicer4-Superbuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `MD5_Init'

Solution:
cd Slicer-superbuild
rm -rf LibArchive-*
make -j4

Details:
* http://na-mic.org/Mantis/view.php?id=1616
* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=18923
* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=18969

=== A tool returned an error code from "Performing configure step for ..." ===

Older CMake versions had some problems building complex projects on Windows7 (see more details in: http://cmake.org/Bug/view.php?id=12957).
Make sure you use the required CMake version.

=== A tool returned an error code from "Performing download step (git clone) for ..." ===

CMake has problems cloning git repositories on Windows7. See more details in http://cmake.org/Bug/view.php?id=12564

If you think the described problem is the same as you have, please add your specific error message to the bug report (the more people report the problem the sooner it will be fixed).

=== No rule to make target `/usr/lib/x86_64-linux-gnu/libGL.so' ===
See http://techtidings.blogspot.com/2012/01/problem-with-libglso-on-64-bit-ubuntu.html

=== X11 Window errors at start time ===
<pre>
X Error: BadWindow (invalid Window parameter) 3
Extension: 137 (Uknown extension)
Minor opcode: 4 (Unknown request)
Resource id: 0x4200199
X Error: BadWindow (invalid Window parameter) 3
Extension: 137 (Uknown extension)
Minor opcode: 4 (Unknown request)
Resource id: 0x42001a6
X Error: BadWindow (invalid Window parameter) 3
Extension: 137 (Uknown extension)
Minor opcode: 4 (Unknown request)
Resource id: 0x42001b3
</pre>

Solution:
* Reinstall Nvidia drivers (that also rewrite the xorg.conf file).

=== error C2061: syntax error : identifier 'ssize_t' ===
<pre>
4>1>Compiling...
4>1>version.c
4>1>c:\chene\winbin64\slicer4\cmcurl\urldata.h(585) : error C2061: syntax error : identifier 'ssize_t'
4>1>c:\chene\winbin64\slicer4\cmcurl\urldata.h(593) : error C2365: 'fread' : redefinition; previous definition was 'function'
4>1> C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\include\stdio.h(248) : see declaration of 'fread'
4>1>c:\chene\winbin64\slicer4\cmcurl\urldata.h(610) : error C2059: syntax error : '}'
</pre>

Solution:
* See [[#A_tool_returned_an_error_code_from_.22Performing_configure_step_for_....22]]

 

==Platform Notes==

* Linux Ubuntu: if you have odd rendering artifacts, try disabling visual effects (System/Appearance/Visual Effects)
* Unix-Like: remember that "make" wrapping calls to pull source makes it very much not idempotent; re-running make after a build error may get past the previously encountered error. Kind of like re-compiling LaTeX many times to fix references.
* Windows: If build was OK, but it Slicer doesn't start (gives the error: [bin/Release/SlicerQT-real.exe] exit abnormally - Report the problem.) then one possible root cause is that you have a copy of Python26.dll in your windows system directory (e.g., c:\Windows\System32\python26.dll). The solution is to rename or remove the python dll in the system directory. See more details here: http://www.na-mic.org/Bug/view.php?id=1180

Documentation/4.1/Modules/Annotations

2012-09-20T18:14:02Z

Pkarasev:

{{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: Nicole Aucoin, BWH 
Contributor: Kilian Pohl, UPenn 
Contributor: Daniel Haehn, UPenn 
Contributors: Yong Zhang, BWH 
Contributor: Alex Yarmarkovich, Isomics 
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
|{{collaborator|logo|nac}}|{{collaborator|longname|nac}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description}}


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

* Use Case 1: placing fiducial markers at points of interest on images
* Use Case 2: using fiducials to seed tractography
* Use Case 3: using rulers to measure tumor diameters
* Use Case 4: using ROIs to crop volume rendering

For the lazy person in a hurry, see below screenshots. Note: this is 4.1.1 slicer version.

{|
[[Image:createFiducialClickHere.png|400px|thumb|left|'''where to click in the GUI to create fiducials:''']]

[[Image:HierKlickenZuEdit.png|400px|thumb|left|'''where to click to edit appearance of a fiducial:''']]
|}


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

To delete multiple fiducials from a list press down the Control key and left click to select fiducials in the Annotations GUI, then click on the trash can to delete them.

To move multiple fiducials from one list to another, hold down the Shift key and left click to select a group of fiducials, then while still holding down the shift key, left click on the selection to drag and drop it.


{{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.

{|
|[[Image:Slicer4-1-Annotations-GUI.jpeg|thumb|200px|Annotations]]
|[[Image:Slicer4-Annotations-ModifyPropeties.jpeg|thumb|200px|Modify Annotation Properties]]
|[[Image:Slicer4-Annotations-ModifyHierarchy.jpeg|thumb|200px|Modify Hierarchy Properties]]
|[[Image:Slicer4-Annotations-Toolbar.jpeg|thumb|200px|Annotation tool bar]]
|}
{{documentation/{{documentation/version}}/module-parametersdescription}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* The Annotations tool bar at the top of the main Slicer window is used to add new annotations to the scene.


{{documentation/{{documentation/version}}/module-section|References}}
N/A


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

=== Access to Fiducial Locations from Python ===

Starting from the ID of an Annotation hierarchy node that collects a group of fiducials, you can get a fiducial location using the following python code:
# get the first list of annotations
listNodeID = "vtkMRMLAnnotationHierarchyNode2"
annotationHierarchyNode = slicer.mrmlScene.GetNodeByID(listNodeID)
# get the first in the list
listIndex = 0
annotation = annotationHierarchyNode.GetNthChildNode(listIndex).GetAssociatedNode()
coords = [0,0,0]
annotation.GetFiducialCoordinates(coords)
print coords

If you have the id of the fiducial node, it's more direct:
fidID = "vtkMRMLAnnotationFiducialNode1"
fid = slicer.mrmlScene.GetNodeByID(fidID)
coords = [0,0,0]
fid.GetFiducialCoordinates(coords)
print coords[0], coords[1], coords[2]

You can also look at the sample code in the [https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Scripts/Endoscopy.py#L287 Endoscopy module] to see how python is used to access fiducials.

=== Transforms ===
Individual annotations are transformable (able to be placed under a transform node), but lists are not. In order to apply a transform to a set of annotations, open the python console (View -> Python Interctor) and use the following code. First you'll need to get the transform node MRML id from the Data module (click on Display MRML IDs), and save it to a variable:
transformNodeID = "vtkMRMLLinearTransformNode5"
Then get the id of the annotation hierarchy list node that holds the annotations that you wish to transform:
listNodeID = "vtkMRMLAnnotationHierarchyNode3"
Then use this code snippet to apply the transform to all the annotations under the hierarchy node:
annotationHierarchyNode = slicer.mrmlScene.GetNodeByID(listNodeID)
numNodes = annotationHierarchyNode.GetNumberOfChildrenNodes()
for i in range(numNodes):
annotation = annotationHierarchyNode.GetNthChildNode(i).GetAssociatedNode()
annotation.SetAndObserveTransformNodeID(transformNodeID)
* [[Documentation/{{documentation/version}}/Modules/Transforms#Information_for_Developers|Read more]] about transforming MRML nodes

=== Programmatic Access to Fiducials ===

This section explains how to access fiducial nodes added into the scene by the user.

In your module's Logic class, overwrite SetMRMLSceneInternal to observe the NodeAddedEvent of the scene:
void vtkSlicerMYMODULEModuleLogic::SetMRMLSceneInternal(vtkMRMLScene * newScene)
{
vtkIntArray *events = vtkIntArray::New();
events->InsertNextValue(vtkMRMLScene::NodeAddedEvent);
// Optionally you can add here more events
// you can be interested in such as vtkMRMLScene::NodeRemovedEvent
this->SetAndObserveMRMLSceneEventsInternal(newScene, events);
events->Delete();
}
Via the set and observe mrml scene macro, anytime a node is added into the scene, it will trigger the base Logic class method
[http://slicer.org/doc/html/classvtkMRMLAbstractLogic.html#a51fdf00ecfc18c1a1465d4bccb789ef1 vtkMRMLAbstractLogic::ProcessMRMLNodesEvents] which calls the virtual method <code>vtkMRMLAbstractLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* node)</code> to reimplement in your logic:
void vtkSlicerMYMODULEModuleLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* addedNode)
{
vtkMRMLAnnotationFiducialNode* fidNode =
vtkMRMLAnnotationFiducialNode::SafeDownCast(addedNode);
if (fidNode)
{
// here you write what you need to do when a
// fiducial node is added into the scene
}
}

===Selection and interaction===
This section indicates how to change in the GUI the mouse placing mode to start placing nodes.

For the selection and interaction nodes, make sure that you access the singleton nodes already in the scene (rather than making your own) via (caveat: this call works on displayable managers, you may have to go a different route to get at the application logic):
vtkMRMLApplicationLogic *mrmlAppLogic = this->GetMRMLApplicationLogic();
vtkMRMLInteractionNode *inode = mrmlAppLogic->GetInteractionNode();
vtkMRMLSelectionNode *snode = mrmlAppLogic->GetSelectionNode();
If you can't get at the mrml application logic, you can get the nodes from the scene:
vtkMRMLInteractionNode *interactionNode = vtkMRMLInteractionNode::SafeDownCast(this->GetMRMLScene()->GetNodeByID("vtkMRMLInteractionNodeSingleton"));

You can then call methods on the nodes or add your own event observers as in
vtkSlicerAnnotationModuleLogic::ObserveMRMLScene
You can see vtkSlicerAnnotationModuleLogic::ProcessMRMLNodesEvents to see how to respond to interaction node changes, but I don't think you'll need to do that.

Slicer4/Base/QTGUI/qSlicerMouseModeToolBar.cxx has a lot of the code you'll need as well, with a slightly different way of getting at the mrml app logic to access the nodes.

The calls you need to make to switch into placing fiducials with the mouse are:
selectionNode->SetActiveAnnotationID ("vtkMRMLAnnotationFiducialNode");
interactionNode->SetCurrentInteractionMode(vtkMRMLInteractionNode::Place);
If you don't set PlaceModePersistence on the interaction node, the mouse mode/current interaction mode will automatically go back to view transform after one fiducial has been placed, and you just need to reset the current interaction mode for future placing (the active annotation id is persistent).


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

Documentation/4.0/Modules/Annotations

2012-09-20T18:11:47Z

Pkarasev: spent a very long time trying to figure out how to add fiducials, docs didn't have an "idiot's quickstart guide" so I added screenshots.

File:HierKlickenZuEdit.png

2012-09-20T17:56:12Z

Pkarasev: very useful place to click: edit the fiducial

very useful place to click: edit the fiducial

File:CreateFiducialClickHere.png

2012-09-20T17:55:18Z

Pkarasev: click here in unlikely place to create a fiducial

click here in unlikely place to create a fiducial

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:14:25Z

Pkarasev: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:
[[Image:curvature_colon_ac.png|thumb|280px|Surface Curvature]]

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location
[[Image:Labels_ac.png|thumb|280px|Region Selection]]

----

===Tutorials===

* Load the scene in the below data set. You will see 6 fiducial points as initializers. Select the module from Modules -> Segmentation -> MeshContourSegmentation. Create a new output model, and apply. It will take a few minutes, due to geometry computation across the entire large mesh.
* [[Media:Meshexample-2010-04-23.zip]]

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

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

{|
|
* '''Input panel:'''
*Input Model: PolyData for input
*Contour Points: Fiducial List to input (Must be "Selected" in Fiducials Module)
*Output Model: The PolyData into which to put the result
*Evolution Iterations: Number of Levelset Iterations
*Mesh Smoothing Iterations: Number of times to pre-smooth the mesh for better geometry computation
*Curvature Averaging Iterations: Number of times to average computed mean curvature and gradient, to make evolution smoother
*Adjacency Tree Levels: How deep of a neighborhood lookup to build. If the mesh is very fine and practically 'flat' everywhere, this must increase. Exponentially slows things down as it is raised (Suggestion: make the mesh as coarse as practical so it can be set to 1 or 0)
*Right Handed Mesh: whether the normal vector needs a negative sign or not.
|[[Image:Sfls_interface.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:14:00Z

Pkarasev: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:
[[Image:curvature_colon_ac.png|thumb|280px|Surface Curvature]]

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location
[[Image:Labels_ac.png|thumb|280px|Region Selection]]

===Tutorials===

* Load the scene in the below data set. You will see 6 fiducial points as initializers. Select the module from Modules -> Segmentation -> MeshContourSegmentation. Create a new output model, and apply. It will take a few minutes, due to geometry computation across the entire large mesh.
* [[Media:Meshexample-2010-04-23.zip]]

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

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

{|
|
* '''Input panel:'''
*Input Model: PolyData for input
*Contour Points: Fiducial List to input (Must be "Selected" in Fiducials Module)
*Output Model: The PolyData into which to put the result
*Evolution Iterations: Number of Levelset Iterations
*Mesh Smoothing Iterations: Number of times to pre-smooth the mesh for better geometry computation
*Curvature Averaging Iterations: Number of times to average computed mean curvature and gradient, to make evolution smoother
*Adjacency Tree Levels: How deep of a neighborhood lookup to build. If the mesh is very fine and practically 'flat' everywhere, this must increase. Exponentially slows things down as it is raised (Suggestion: make the mesh as coarse as practical so it can be set to 1 or 0)
*Right Handed Mesh: whether the normal vector needs a negative sign or not.
|[[Image:Sfls_interface.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:12:36Z

Pkarasev: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location
[[Image:Labels_ac.png]]

===Tutorials===

* Load the scene in the below data set. You will see 6 fiducial points as initializers. Select the module from Modules -> Segmentation -> MeshContourSegmentation. Create a new output model, and apply. It will take a few minutes, due to geometry computation across the entire large mesh.
* [[Media:Meshexample-2010-04-23.zip]]

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

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

{|
|
* '''Input panel:'''
*Input Model: PolyData for input
*Contour Points: Fiducial List to input (Must be "Selected" in Fiducials Module)
*Output Model: The PolyData into which to put the result
*Evolution Iterations: Number of Levelset Iterations
*Mesh Smoothing Iterations: Number of times to pre-smooth the mesh for better geometry computation
*Curvature Averaging Iterations: Number of times to average computed mean curvature and gradient, to make evolution smoother
*Adjacency Tree Levels: How deep of a neighborhood lookup to build. If the mesh is very fine and practically 'flat' everywhere, this must increase. Exponentially slows things down as it is raised (Suggestion: make the mesh as coarse as practical so it can be set to 1 or 0)
*Right Handed Mesh: whether the normal vector needs a negative sign or not.
|[[Image:Sfls_interface.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:11:25Z

Pkarasev: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location

===Tutorials===

* Load the scene in the below data set. You will see 6 fiducial points as initializers. Select the module from Modules -> Segmentation -> MeshContourSegmentation. Create a new output model, and apply. It will take a few minutes, due to geometry computation across the entire large mesh.
* [[Media:Meshexample-2010-04-23.zip]]

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

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

{|
|
* '''Input panel:'''
*Input Model: PolyData for input
*Contour Points: Fiducial List to input (Must be "Selected" in Fiducials Module)
*Output Model: The PolyData into which to put the result
*Evolution Iterations: Number of Levelset Iterations
*Mesh Smoothing Iterations: Number of times to pre-smooth the mesh for better geometry computation
*Curvature Averaging Iterations: Number of times to average computed mean curvature and gradient, to make evolution smoother
*Adjacency Tree Levels: How deep of a neighborhood lookup to build. If the mesh is very fine and practically 'flat' everywhere, this must increase. Exponentially slows things down as it is raised (Suggestion: make the mesh as coarse as practical so it can be set to 1 or 0)
*Right Handed Mesh: whether the normal vector needs a negative sign or not.
|[[Image:Sfls_interface.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:10:52Z

Pkarasev: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location

===Tutorials===

* Load the scene in the below data set. You will see 6 fiducial points as initializers. Select the module from Modules -> Segmentation -> MeshContourSegmentation. Create a new output model, and apply. It will take a few minutes, due to geometry computation across the entire large mesh.
* [[Media:Meshexample-2010-04-23.zip]]

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

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

{|
|
* '''Input panel:'''
Input Model: PolyData for input
Contour Points: Fiducial List to input (Must be "Selected" in Fiducials Module)
Output Model: The PolyData into which to put the result

Evolution Iterations: Number of Levelset Iterations
Mesh Smoothing Iterations: Number of times to pre-smooth the mesh for better geometry computation
Curvature Averaging Iterations: Number of times to average computed mean curvature and gradient, to make evolution smoother
Adjacency Tree Levels: How deep of a neighborhood lookup to build. If the mesh is very fine and practically 'flat' everywhere, this must increase. Exponentially slows things down as it is raised (Suggestion: make the mesh as coarse as practical so it can be set to 1 or 0)
Right Handed Mesh: whether the normal vector needs a negative sign or not.
|[[Image:Sfls_interface.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:06:50Z

Pkarasev: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location

===Tutorials===

* Load the scene in the below data set. You will see 6 fiducial points as initializers. Select the module from Modules -> Segmentation -> MeshContourSegmentation. Create a new output model, and apply. It will take a few minutes, due to geometry computation across the entire large mesh.
* [[Media:Meshexample-2010-04-23.zip]]

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:Sfls_interface.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:05:50Z

Pkarasev: /* Tutorials */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location

===Tutorials===

* Load the scene in the below data set. You will see 6 fiducial points as initializers. Select the module from Modules -> Segmentation -> MeshContourSegmentation. Create a new output model, and apply. It will take a few minutes, due to geometry computation across the entire large mesh.
* [[Media:Meshexample-2010-04-23.zip]]

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

File:Meshexample-2010-04-23.zip

2010-05-02T21:04:06Z

Pkarasev:

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T21:02:51Z

Pkarasev: /* Notes from the Developer(s) */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location

===Tutorials===

* Tutorial 1
* Data Set 1

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

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

- Give it some seed points for initialization.

- Seed points do *NOT* need to be 'in order', but of course the closer they are to the expected final result, the better.

- The region being marked as initial should be convex.

- The initial contour is formed like this: connect all seed points to eachother, and fill the convex hull. The boundary of this convex fill is the initial contour.

- Slow part of the computation: forming adjacency tree for curvature computation. The parameter "adjacency levels" says how many levels to branch out from each vertex when fitting paraboloid. These neighbors are stored, because they are needed when computing the curve geometry during levelset evolution.

- Output: MeanCurvature is scaled to [-256,256] and displayed everywhere. The ActiveContourVertices array gives the location of segmented region on the mesh.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T20:56:29Z

Pkarasev: /* Source code & documentation */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Karol Chudy (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:

2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location

===Tutorials===

* Tutorial 1
* Data Set 1

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

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

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

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

-Only VTK & STL

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/ All Code]

Several Key Points:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/SparseFieldLevelSetContour.cxx Entry Point from Slicer]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkInitClosedPath.cxx Computation of Initial Path from Un-Ordered Initial Points]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkComputeLocalGeometry.cxx Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/vtkLevelSetMeshEvolver.cxx Levelset Evolution Entry Point]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/SparseFieldLevelSetContour/LSops.cxx Levelset Evolution Core]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkComputeLocalGeometry.html Compute Local Geometry]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkInitClosedPath.html Initialize Closed Path from Fiducial Points]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLevelSetMeshEvolver.html Levelset Mesh Evolver]

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T20:52:28Z

Pkarasev: /* Source code & documentation */

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T20:50:19Z

Pkarasev: /* Source code & documentation */

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T20:44:42Z

Pkarasev: /* Dependencies */

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T20:43:31Z

Pkarasev: /* Tests */

File:Sfls interface.png

2010-05-02T20:39:18Z

Pkarasev:

File:Curvature colon ac.png

2010-05-02T20:29:03Z

Pkarasev:

File:Labels ac.png

2010-05-02T20:28:41Z

Pkarasev:

File:Surface H c.png

2010-05-02T19:00:46Z

Pkarasev:

Modules:MeshContourSegmentation-Documentation-3.6

2010-05-02T18:59:14Z

Pkarasev: /* Use Cases, Examples */

Modules:MeshContourSegmentation-Documentation-3.6

2010-04-01T19:38:37Z

Pkarasev: /* Authors, Collaborators & Contact */

Documentation/3.6

2010-04-01T19:37:34Z

Pkarasev: /* Surface Models */

This is work in progress

=Main GUI=

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

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

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

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

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

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

==Specialized Modules==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

====Example Extensions====

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

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

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

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

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

'''Deprecated Extensions'''

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

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

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

Modules:GyriContourSegmentation-Documentation-3.5

2010-04-01T19:36:53Z

Pkarasev:

[[Documentation-3.6|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Mesh Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

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

===Tutorials===

* Tutorial 1
* Data Set 1

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

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

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

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

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

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

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

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:MeshContourSegmentation-Documentation-3.6

2010-04-01T19:36:39Z

Pkarasev: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Mesh Contour Segmentation=== MyModule {| |Surface Normal Curvature |[[Imag…'

Modules:GyriContourSegmentation-Documentation-3.5

2010-04-01T19:30:26Z

Pkarasev:

Modules:GyriContourSegmentation-Documentation-3.5

2010-04-01T19:29:46Z

Pkarasev: /* Development */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

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

===Tutorials===

* Tutorial 1
* Data Set 1

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

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

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

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

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

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

===Source code & documentation===

Links to the module's source code:

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

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

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2010-04-01T19:28:51Z

Pkarasev: /* Quick Tour of Features and Use */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

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

===Tutorials===

* Tutorial 1
* Data Set 1

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

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

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2010-04-01T19:28:19Z

Pkarasev: /* Usage */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

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

===Tutorials===

* Tutorial 1
* Data Set 1

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2010-04-01T19:27:26Z

Pkarasev: /* Examples, Use Cases & Tutorials */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

===Use Cases, Examples===

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2010-04-01T19:27:04Z

Pkarasev: /* Examples, Use Cases & Tutorials */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Documentation/3.6

2010-04-01T19:23:41Z

Pkarasev: /* Surface Models */

This is work in progress

=Main GUI=

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

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

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

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

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

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

==Specialized Modules==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

====Example Extensions====

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

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

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

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

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

'''Deprecated Extensions'''

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

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

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

Documentation/3.6

2010-04-01T19:22:23Z

Pkarasev: /* List of Modules added or significantly revised since the 3.4 release */

This is work in progress

=Main GUI=

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

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

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

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

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

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

==Specialized Modules==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

====Example Extensions====

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

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

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

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

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

'''Deprecated Extensions'''

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

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

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

Modules:GyriContourSegmentation-Documentation-3.5

2009-12-04T23:52:11Z

Pkarasev: /* Acknowledgment */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from
NIH (NAC P41 RR-13218) through Brigham and Women’s
Hospital. An NSF Fellowship supported part of the work.

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2009-12-04T23:49:56Z

Pkarasev: /* References */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

===References===

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

File:Pkmesh-spie.pdf

2009-12-04T23:48:40Z

Pkarasev:

Modules:GyriContourSegmentation-Documentation-3.5

2009-12-04T23:48:11Z

Pkarasev: /* References */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2009-12-04T23:47:42Z

Pkarasev: /* References */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum.
User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
[[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2009-12-04T23:47:27Z

Pkarasev: /* References */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010. [[File:pkmesh-spie.pdf]]

Modules:GyriContourSegmentation-Documentation-3.5

2009-12-04T23:29:24Z

Pkarasev: /* Module Description */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
__NOTOC__
===Gyri Contour Segmentation===
MyModule

{|
|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Peter Karasev (Author): Georgia Tech
* Allen Tannenbaum (Collaborator): Georgia Tech
* Ron Kikinis (Collaborator): Harvard Medical School SPL
* Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
* Contact: Peter Karasev, pkarasev@gatech.edu

===Module Description===
This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

Modules:GyriContourSegmentation-Documentation-3.5

2009-12-04T23:01:15Z

Pkarasev: /* Gyri Contour Segmentation */

File:Tumor conv 3.png

2009-12-04T22:52:40Z

Pkarasev:

File:Tumor2 init 4.PNG

2009-12-04T22:52:31Z

Pkarasev:

File:Sulci6 done2.png

2009-12-04T22:52:22Z

Pkarasev:

File:Sulci3 init 3.png

2009-12-04T22:52:09Z

Pkarasev:

File:Sulci3 conv 2.PNG

2009-12-04T22:51:54Z

Pkarasev:

File:Curvature bumps1 good.png

2009-12-04T22:51:44Z

Pkarasev: