Slicer Wiki - User contributions [en]

File:Slide test3.pdf

2011-01-31T22:59:54Z

Mmaddah:

File:Slide test2.pdf

2011-01-31T22:59:38Z

Mmaddah:

File:Slide test1.pdf

2011-01-31T22:59:20Z

Mmaddah:

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-31T22:59:05Z

Mmaddah:

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|[[File:test1p.png|thumb|560px|An example of DTI fiber clustering and tract-oriented quantitative analysis]]
|}

===Installation===

To add the module to an installed binary of slicer (3.6.2 and later):

* 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.
* Select '''EM Fiber Clustering''' to install and click to download. The installed extension, Fiber Clustering and Analysis, will be available when you restart slicer under Modules --> Diffusion --> Tractography.

Please report any installation problem to Mahnaz Maddah (mmaddah at alum.mit.edu)

===Instructions and Test Data===

== Single-Subject ==

Clustering of the cingulum fiber tracts, Test1 Data: [[Media:single_subject.tar.gz]], Guide: [[Media:slide_test1.pdf]]

== Single-Subject with Atlas-Based Seeding ==

Clustering of the uncinate fasciculus tract using the SRI24 atlas, Test2 Data: [[Media:atlas_based_seeding.tar.gz]], Guide: [[Media:slide_test2.pdf]]

== Multi-Subject ==

Clustering of the genu in multiple subjects, Test3 Data: [[Media:multi-subject.tar.gz]], Guide: [[Media:slide_test3.pdf]]

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-31T19:37:05Z

Mmaddah: /* Multi-Subject */

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|[[File:test1p.png|thumb|560px|An example of DTI fiber clustering and tract-oriented quantitative analysis]]
|}

===Installation===

To add the module to an installed binary of slicer (3.6.2 and later):

* 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.
* Select '''EM Fiber Clustering''' to install and click to download. The installed extension, Fiber Clustering and Analysis, will be available when you restart slicer under Modules --> Diffusion --> Tractography.

Please report any installation problem to Mahnaz Maddah (mmaddah at alum.mit.edu)

===Instructions and Test Data===

== Single-Subject ==

Test1 Data - Clustering of the cingulum fiber tracts [[Media:single_subject.tar.gz]]

== Single-Subject with Atlas-Based Seeding ==

Test2 Data - Clustering of the uncinate fasciculus tract using the SRI24 atlas [[Media:atlas_based_seeding.tar.gz]]

== Multi-Subject ==

Test3 Data - Clustering of the genu in multiple subjects [[Media:multi-subject.tar.gz]]

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-31T18:09:32Z

Mmaddah: /* Single-Subject */

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|[[File:test1p.png|thumb|560px|An example of DTI fiber clustering and tract-oriented quantitative analysis]]
|}

===Installation===

To add the module to an installed binary of slicer (3.6.2 and later):

* 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.
* Select '''EM Fiber Clustering''' to install and click to download. The installed extension, Fiber Clustering and Analysis, will be available when you restart slicer under Modules --> Diffusion --> Tractography.

Please report any installation problem to Mahnaz Maddah (mmaddah at alum.mit.edu)

===Instructions and Test Data===

== Single-Subject ==

Test1 Data - Clustering of the cingulum fiber tracts [[Media:single_subject.tar.gz]]

== Single-Subject with Atlas-Based Seeding ==

Test2 Data - Clustering of the uncinate fasciculus tract using the SRI24 atlas [[Media:atlas_based_seeding.tar.gz]]

== Multi-Subject ==

Test3 Data - Clustering of the genu using the SRI24 atlas [[Media:multi-subject.tar.gz]]

File:Multi-subject.tar.gz

2011-01-31T18:02:34Z

Mmaddah:

File:Atlas based seeding.tar.gz

2011-01-31T18:01:48Z

Mmaddah:

File:Single subject.tar.gz

2011-01-31T18:00:59Z

Mmaddah:

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-31T18:00:10Z

Mmaddah:

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|[[File:test1p.png|thumb|560px|An example of DTI fiber clustering and tract-oriented quantitative analysis]]
|}

===Installation===

To add the module to an installed binary of slicer (3.6.2 and later):

* 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.
* Select '''EM Fiber Clustering''' to install and click to download. The installed extension, Fiber Clustering and Analysis, will be available when you restart slicer under Modules --> Diffusion --> Tractography.

Please report any installation problem to Mahnaz Maddah (mmaddah at alum.mit.edu)

===Instructions and Test Data===

== Single-Subject ==

Test1 Data - Clustering of the Cingulum fiber tracts [[Media:single_subject.tar.gz]]

== Single-Subject with Atlas-Based Seeding ==

Test2 Data - Clustering of the uncinate fasciculus tract using the SRI24 atlas [[Media:atlas_based_seeding.tar.gz]]

== Multi-Subject ==

Test3 Data - Clustering of the genu using the SRI24 atlas [[Media:multi-subject.tar.gz]]

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-28T01:14:07Z

Mmaddah: /* Installation */

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|[[File:test1p.png|thumb|560px|An example of DTI fiber clustering and tract-oriented quantitative analysis]]
|}

===Installation===

To add the module to an installed binary of slicer (3.6.2 and later):

* 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.
* Select '''EM Fiber Clustering''' to install and click to download. The installed extension, Fiber Clustering and Analysis, will be available when you restart slicer under Modules --> Diffusion --> Tractography.

Please report any installation problem to Mahnaz Maddah (mmaddah at alum.mit.edu)

===Instructions and Test Data===

== Single-Subject ==

== Single-Subject with Atlas-Based Seeding ==

== Multi-Subject ==

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-28T01:12:45Z

Mmaddah: /* Instructions and Test Data */

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-28T01:12:22Z

Mmaddah: /* Installation */

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-27T23:52:51Z

Mmaddah: /* Module Name */

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-27T23:51:10Z

Mmaddah: /* Module Name */

File:Test1p.png

2011-01-27T23:50:36Z

Mmaddah:

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-27T19:15:46Z

Mmaddah: /* Module Name */

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|}

===Installation===

To add the module to an installed binary of slicer (3.6.2 and later):

* 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.
* Select '''EM Fiber Clustering''' to install and click to download. The installed extension, Fiber Clustering and Analysis, will be available when you restart slicer under Modules --> Diffusion --> Tractography.

Please report any installation problem to mmaddah@alum.mit.edu

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-12T18:31:12Z

Mmaddah: /* Module Name */

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|}

File:ModuleInterface.png

2011-01-12T16:18:21Z

Mmaddah:

DTI Fiber Clustering Module-Documentation-3.6.2

2011-01-12T16:16:28Z

Mmaddah: Created page with '===Module Name=== Fiber Clustering and Analysis (EM Fiber Clustering) Module {| |Module interface |[[File:shot2.png|thumb|280px|Traject…'

===Module Name===
Fiber Clustering and Analysis (EM Fiber Clustering) Module

{|
|[[File:moduleInterface.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

Modules:EMDTIClustering-Documentation-3.6

2010-12-18T00:32:58Z

Mmaddah: /* Module Name */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

'''For version 3.6.2 and beyond, please refer to [[DTI Fiber Clustering Module-Documentation-3.6.2]].''' The new version has two new capabilities: Atlas-based seeding and multi-subject tract-based quantitative analysis.

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, mmaddah [at] alum.mit.edu

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

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

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work:
Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.

===Dependencies===

NA

===Tests===

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

* Test [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti EMClusteringTest.cxx]

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===
This work has been supported by NAC.

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.6

2010-12-18T00:31:50Z

Mmaddah: /* Module Name */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

'''For version 3.6.2 and beyond, please refer to [[EM DTI Fiber Clustering Module-Documentation-3.6.2]].''' The new version has two new capabilities: Atlas-based seeding and multi-subject tract-based quantitative analysis.

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, mmaddah [at] alum.mit.edu

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

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

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work:
Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.

===Dependencies===

NA

===Tests===

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

* Test [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti EMClusteringTest.cxx]

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===
This work has been supported by NAC.

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Documentation/3.6

2010-05-10T18:59:56Z

Mmaddah: /* Slicer Extensions */

=Documentation Draft notes=
Key for flagged modules below:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
* for interactive modules, see other modules in Base/GUI for an example.

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

=Introduction=

3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications.

3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.

The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)

The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes. The community contributing to Slicer 3.6 is and the following [[Announcments-3.6-Team|acknowledged here]].

*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].
*For sample data see [[SampleData|here]]

=Main GUI=

*[[Image:WeakDoc.png]][[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=

==Core==
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
*Fast Registration
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust Registration
**[[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]]: automated registration (rigid to affine to nonrigid) with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
*Brain Only Registration
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data Registration
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

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

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak)
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Slicer Extensions==

'''Introduction'''
* Slicer Extensions are a mechanism for anybody, including 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

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Quantification
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[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.

'''Info for Developers'''

*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.

*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]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

=Other information=

'''Developer Tools'''
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

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

'''Non-SPL Supported Compatibility Packages'''
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

'''QA Table'''

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

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

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

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

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

Modules:EMDTIClustering-Documentation-3.6

2010-05-10T18:58:48Z

Mmaddah: /* Authors, Collaborators & Contact */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, mmaddah [at] alum.mit.edu

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

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

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work:
Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.

===Dependencies===

NA

===Tests===

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

* Test [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti EMClusteringTest.cxx]

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===
This work has been supported by NAC.

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.6

2010-05-04T14:45:56Z

Mmaddah:

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

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

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work:
Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.

===Dependencies===

NA

===Tests===

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

* Test [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti EMClusteringTest.cxx]

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===
This work has been supported by NAC.

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.6

2010-04-28T19:06:57Z

Mmaddah: /* Acknowledgment */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

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

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work:
Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.

===Dependencies===

NA

===Tests===

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

* Test [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti EMClusteringTest.cxx]

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===
This work has been supported by NAC.

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.6

2010-04-28T19:06:21Z

Mmaddah: /* Tests */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

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

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work:
Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.

===Dependencies===

NA

===Tests===

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

* Test [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti EMClusteringTest.cxx]

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.6

2010-04-14T15:35:19Z

Mmaddah: /* Development */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

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

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work:
Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.

===Dependencies===

NA

===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===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Documentation/3.6

2010-04-14T14:43:09Z

Mmaddah: /* Listing of plug-ins */

This is work in progress

=Main GUI=

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

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

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

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

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

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']]
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) [[Modules:Slices-Documentation-3.6|'''3.6 in process''']]
*[[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) '''3.6 in progress'''
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) '''3.6 In Progress'''

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

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

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

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

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

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

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

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

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

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

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

=Slicer Extensions=

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

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

====Example Extensions====

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

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

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

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

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

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

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

=QA=
[[Slicer-3.6-QA|Slicer 3.6 QA table]]

Modules:EMDTIClustering-Documentation-3.6

2010-04-14T14:42:13Z

Mmaddah:

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.6

2010-04-14T14:41:51Z

Mmaddah: Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Module Name=== EM Fiber Clustering Module …'

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.5

2009-11-25T16:57:00Z

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

Modules:EMDTIClustering-Documentation-3.5

2009-11-25T16:56:21Z

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

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

File:Shot2.png

2009-11-24T21:17:28Z

Mmaddah:

File:Shot1.png

2009-11-24T21:16:43Z

Mmaddah:

Modules:EMDTIClustering-Documentation-3.5

2009-11-24T21:15:30Z

Mmaddah: /* Module Name */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform tract-oriented quantitative analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Iterations'' Number of EM Iterations.
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space resolution'' Space resolution for distance map calculation.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.5

2009-11-24T20:38:53Z

Mmaddah: /* Module Name */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot2.JPG|thumb|280px|Trajectories colored by their cluster ID]]
|[[File:shot3.JPG|thumb|280px|Final cluster centers colored by the mean FA along the bundles]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform tract-oriented quantitative analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Iterations'' Number of EM Iterations.
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space resolution'' Space resolution for distance map calculation.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

File:Screenshot1.png

2009-11-24T20:37:28Z

Mmaddah: uploaded a new version of "File:Screenshot1.png"

File:Screenshot1.png

2009-11-24T20:32:35Z

Mmaddah: uploaded a new version of "File:Screenshot1.png": Reverted to version as of 20:29, 24 November 2009

File:Screenshot1.png

2009-11-24T20:29:30Z

Mmaddah: uploaded a new version of "File:Screenshot1.png"

File:Screenshot1.png

2009-11-24T20:29:08Z

Mmaddah: uploaded a new version of "File:Screenshot1.png"

File:Screenshot1.png

2009-11-24T20:23:36Z

Mmaddah:

Modules:EMDTIClustering-Documentation-3.5

2009-11-24T20:23:17Z

Mmaddah: /* Module Name */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:screenshot1.png|thumb|280px|Module Interface]]
|[[File:shot2.JPG|thumb|280px|Trajectories colored by their cluster ID]]
|[[File:shot3.JPG|thumb|280px|Final cluster centers colored by the mean FA along the bundles]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform tract-oriented quantitative analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Iterations'' Number of EM Iterations.
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space resolution'' Space resolution for distance map calculation.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.5

2009-11-24T20:21:34Z

Mmaddah: /* Module Name */

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.JPG|thumb|280px|Module Interface]]
|[[File:shot2.JPG|thumb|280px|Trajectories colored by their cluster ID]]
|[[File:shot3.JPG|thumb|280px|Final cluster centers colored by the mean FA along the bundles]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform tract-oriented quantitative analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Iterations'' Number of EM Iterations.
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space resolution'' Space resolution for distance map calculation.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

Modules:EMDTIClustering-Documentation-3.5

2009-11-24T19:57:44Z

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

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[Image:shot1.JPG|thumb|280px|Module Interface]]
|[[Image:shot2.JPG|thumb|280px|Trajectories colored by their cluster ID]]
|[[Image:shot3.JPG|thumb|280px|Final cluster centers colored by the mean FA along the bundles]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform tract-oriented quantitative analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Iterations'' Number of EM Iterations.
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space resolution'' Space resolution for distance map calculation.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

CSVfilesDescription

2009-11-24T19:55:53Z

Mmaddah:

For each cluster, the EM Clustering Module generates a set of CSV files. Let’s first define a couple of terms:

N_[clusterID] : number of significant trajectories that belong to cluster [clusterID].

L_[clusterID] : number of samples along the cluster centerline.

'-1': the missing data.

Now, the description of each file is as follows:

[prefix]_posterior[clusterID].csv

A single column (N_[clusterID] x 1) whose each element is the membership probability of a trajectory in that cluster.

[prefix]_FA_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of Fractional Anisotropy (FA)
for trajectory r corresponding to sample c of the cluster centerline.

[prefix]_MD_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of Mean Diffusivity (MD)
for trajectory r corresponding to sample c of the cluster centerline.

[prefix]_Par_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of parallel diffusivity (largest Eigen value of the tensor matrix)
for trajectory r corresponding to sample c of the cluster centerline.

[prefix]_Per_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of perpendicular diffusivity (mean value of the two Eigen values
- other than the largest one - of the tensor matrix) for trajectory r corresponding to sample c of the cluster centerline.

Matlab scripts [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/ProcessingScripts/?root=quantitativedti here] can be used to generate plots of diffusion parameters along each cluster.

Modules:EMDTIClustering-Documentation-3.5

2009-11-24T19:18:07Z

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

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[Image:shot1.JPG|thumb|280px|Module Interface]]
|[[Image:shot2.JPG|thumb|280px|Trajectories colored by their cluster ID]]
|[[Image:shot3.JPG|thumb|280px|Final cluster centers colored by the mean FA along the bundles]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided either by passing a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform tract-oriented quantitative analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Iterations'' Number of EM Iterations.
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space resolution'' Space resolution for distance map calculation.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

CSVfilesDescription

2009-11-24T19:16:34Z

Mmaddah:

For each cluster, the EM Clustering Module generates a set of CSV files. Let’s first define a couple of terms:

N_[clusterID] : number of significant trajectories that belong to cluster [clusterID].

L_[clusterID] : number of samples along the cluster centerline.

'-1': the missing data.

Now, the description of each file is as follows:

[prefix]_posterior[clusterID].csv

A single column (N_[clusterID] x 1) whose each element is the membership probability of a trajectory in that cluster.

[prefix]_FA_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of Fractional Anisotropy (FA)
for trajectory r corresponding to sample c.

[prefix]_MD_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of Mean Diffusivity (MD)
for trajectory r corresponding to sample c.

[prefix]_Par_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of parallel diffusivity (largest Eigen value of the tensor matrix)
for trajectory r corresponding to sample c.

[prefix]_Per_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of perpendicular diffusivity (mean value of the two Eigen values
- other than the largest one - of the tensor matrix) for trajectory r corresponding to sample c.

Matlab scripts [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/ProcessingScripts/?root=quantitativedti here] can be used to generate plots of diffusion parameters along each cluster.

CSVfilesDescription

2009-11-24T19:10:04Z

Mmaddah: Created page with 'For each cluster, the EM Clustering Module generates a set of CSV files. Let’s first define a couple of terms: N_[clusterID] : number of significant trajectories that belong …'

For each cluster, the EM Clustering Module generates a set of CSV files. Let’s first define a couple of terms:

N_[clusterID] : number of significant trajectories that belong to cluster [clusterID].

L_[clusterID] : number of samples along the cluster centerline.

'-1': the missing data.

Now, the description of each file is as follows:

[prefix]_posterior[clusterID].csv

A single column (N_[clusterID] x 1) whose each element is the membership probability of a trajectory in that cluster.

[prefix]_FA_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of Fractional Anisotropy (FA)
for trajectory r corresponding to sample c.

[prefix]_MD_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of Mean Diffusivity (MD)
for trajectory r corresponding to sample c.

[prefix]_Par_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of parallel diffusivity (largest Eigen value of the tensor matrix)
for trajectory r corresponding to sample c.

[prefix]_Per_cluster[clusterID].csv

A matrix (N_[clusterID] x L_[clusterID]) whose each element(r,c) is the value of perpendicular diffusivity (mean value of the two Eigen values
- other than the largest one - of the tensor matrix) for trajectory r corresponding to sample c.

Modules:EMDTIClustering-Documentation-3.5

2009-11-24T18:59:51Z

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

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

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

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[Image:shot1.JPG|thumb|280px|Module Interface]]
|[[Image:shot2.JPG|thumb|280px|Trajectories colored by their cluster ID]]
|[[Image:shot3.JPG|thumb|280px|Final cluster centers colored by the mean FA along the bundles]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided either by passing a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform tract-oriented quantitative analysis" is flaged .
''Perform tract-oriented quantitative analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Iterations'' Number of EM Iterations.
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space resolution'' Space resolution for distance map calculation.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that can contribute to new center formation.

== Development ==

===Dependencies===

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]