Slicer Wiki - User contributions [en]

Slicer4:VisualBlog

2014-01-09T23:03:43Z

Reckbo2:

This is the Slicer 4 visual blog. Please click [[Slicer3:VisualBlog| here]] if you are looking for the old Slicer 3 visual blog.

<gallery caption="2013" widths="200px" perrow="4">
Image:UKFTractography_CC.jpg|[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/UKFTractography UKFTractography] is a module for computing tractography of DWI images using an unscented Kalman filter. Because of its 2-tensor algorithm, it is able to model fiber crossings and capture many more fibers than a single tensor algorithm.
Image:SPV1.png|[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/ShapePopulationViewer ShapePopulationViewer] is an external tool that allows the user to dynamically interact with multiple surfaces at the same time : an interesting tool for shape visualisation and comparison. It now is available as a Slicer Extension.
Image:SlicerRT_0.13_SubjectHierarchy_ProstateEclipseLoaded.png|[http://www.na-mic.org/Wiki/index.php/2014_Winter_Project_Week:SubjectHierarchy The Subject hierarchy module and mechanism] organizes and handles loaded data in the RT extension package, providing processing and analysis features through plugins. It aspires to be a convenient central organizing point for many of the operations that 3D Slicer and its extensions perform.
Image:DownloadFile 2.jpg|[[Documentation/4.3/Modules/DataStore|The Data Store]] allows a user to easily upload and download MRB files.
Image:SlicerRT ContourRepresentations.png|[[Documentation/4.3/Modules/Contours|The Contours module]] manages contours in the RT extension package.
Image:MultiVolume-4.3.0-update.png| [[Documentation/4.3/Modules/MultiVolumeExplorer|MultiVolumeExplorer module]] has been updated to include the capability to plot multivolume pixel values from 2 multivolumes at the same time. This feature is particularly helpful while visualizing the results of model fits, such as those produced by the updated [[Documentation/4.3/Modules/PkModeling|PkModeling extension]].
Image:MatlabBridgeLogo.png| A new extension allows to run matlab scripts without having to recompile Slicer. For more information see [[Documentation/Nightly/Extensions/MatlabBridge|'''here''']]
Image:ExtensionManagerScreen Shot 2013-05-23 at 9.40.23 PM.png| Extension Manager, the slicer multiplatform Appstore is open for business and free.
Image:ScreenshotLobeSegmentation.png| Semi-automatic lobe segmentation for regional lung disease analysis as part of the Chest Imaging Platform funded by NHLBI 1R01HL116931
Image:CMRToolkit.png|The [[Documentation/4.3/Modules/CARMACARMA| Cardiac MR Extension]] provides tools for segmentation and analysis of heart tissue and structure for treatment and diagnosis of Atrial Fibrillation.
</gallery>
<gallery caption="2012" widths="200px" perrow="4">
Image:BoxChart.png| A box plot
Image:2012-09-07-FetalBrain.png| Fetal brain development. The visualization is using volume rendering and the Multivolume modules in Slicer 4. Click [[media:FetalBrainGowth.mov|'''here''']] for the full movie (~24mb). Data downloaded from [http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Fetal Imperial College].
Image:Screen Shot 2012-09-05 at 10.01.35 AM.png|Leveraging multi viewer layout to arrange 6 slices in the 3D viewer
Image:ComplexQueryWithImage.jpg|Visualization of complex query "motor system + mass + straight gyrus" using the faceted query module
Image:Screen Shot 2012-05-30 at 8.03.23 AM.png| Fibers colored by their mean orientation is now available in the Tractography Display module
Image:SlicerRT-0.2_screenshot.png|[https://www.assembla.com/spaces/slicerrt/milestones/1089853-slicerrt-0-2-release SlicerRT 0.2] has been released! [https://www.assembla.com/spaces/slicerrt/ SlicerRT] is 3D Slicer with extensions for radiotherapy research, which is developed by SparKit project with the contributions from Slicer community.
Image:Screen Shot 2012-04-11 at 8.07.36 AM.png|The new extension manager
Image:Screen Shot 2012-04-11 at 8.11.59 AM.png|Up to date download statistics
Image:Screen Shot 2012-04-05 at 11.35.08 AM.png|A combination of ROI cropping of streamlines, fiducial based seeding and labelmap seeding allows to assess the deformation of streamlines which are due to tumor based deformations.
Image:2012-03-05-downloadpage.png|New download page which highlights the operating system of the downloading system.
Image:2012-03-04-Welcome.png|New look for the Welcome module and the "Load/Save" toolbar
Image:2012-03-04-DWI2FBT.png|Step one of the DWI to Full-brain tractography wizard
Image:2012-03-04-SliceViewerControllers.png|Improved 2-stage user interface for the Slice Viewer Controllers
Image:2012-03-04-DicomWidget.png|Updated Dicom Module
Image:2012-03-04-CoreModuleIcons.png|Updated Icons for the Core Modules
Image:2012-03-04-CompareViews.png|Updated CompareViewers and Viewer Controler Module
Image:Screen Shot 2012-02-23 at 7.53.51 AM.png|MultiVolumeExplorer with support for charting. See [[Documentation/Snapshot/Modules/MultiVolumeExplorer|here]] for more information.
Image:Screen Shot 2012-02-09 at 10.11.08 AM.png|[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] with charting and visualization
Image:3D Slicer 4.0.1.2012-02-03 180.png|Image Quantification with Label Statistics, Charting, and Volume Rendering
Image:Slicer2011-gource.png|Frame from a movie of slicer code activity in 2011. See '''[http://boggs.bwh.harvard.edu/slicer/slicer4-2011-gource.x264.mp4 the full movie here]'''. Made with [http://code.google.com/p/gource/ gource]. Inspired by a [http://vimeo.com/33989053 an ITKv4 gource movie]
Image:AnEarlyChartView.png|A ChartView using QWebView and jqPlot with plots defined in MRML
Image:ALaterChartView.png|A ChartView using QWebView and jqPlot with plots defined in MRML
Image:ABarChartView.png|A bar chart tie MRML to a QWebView
</gallery>
<gallery caption="2011" widths="200px" perrow="4">
Image:Prostate multiparametric visualization Slicer4.png|Compareviewers
Image:Slicer4_ChangeTracker_Ad.png|ChangeTracker visualization of analysis results
Image:Slicer4-SceneViewGUI.jpeg|Sceneview Module
Image:Selection 142.png|Dicom widget
Image:3D Slicer 4.0.gamma-2011-10-20 141.png|Endoscopy module
Image:VolumeRendering-CTA-2011.png|Volumerendering of a CT angiogram
Image:Tumor-Volume-Rendering-PostGad-2011.png|Volumerendering of a subvolume of a post Gadolinium T1 weighted image of a GBM. Note the relation of surrounding vessels to the tumor.
Image:2011-11-12-CroppingWholeBrainTractography-detail.png|Note the deformation of the corpus callosum fibers
Image:2011-11-12-CroppingWholeBrainTractography.png|Using an ROI to crop streamlines from a whole brain tractography. The streamlines display color by orientation, the ellipsoids are displaying fractional anisotropy.
Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|Annotation module 2011-11
Image:MainGUI-2011-11.png|Main Gui with pop-up slice controllers
Image:DataProbe-2011-11.png|The Data Probe
Image:ModelsModule-2011-11.png|Models organized in a hierarchy
Image:Conventional-Widescreen-10-2011.png|New Look Oct 2011
Image:QSlicerVolumeRenderingModule-DualView.png|Dual camera, dual 3D viewer
Image:4.0-Main-GUI-Facelift.png|After the facelift for the GUI
Image:QSlicerModelsModule.png|New models module appearance
Image:SlicerWithVolumeRendering.png|Slicer4 with Volume Rendering
Image:Slicer4-AnnotationGUI.jpg|Slicer4 Annotation Module
Image:SlicerWithDTI.png|Glyph display on cross-sections
Image:FirstCompareViewInSlicer4-2011.png| First CompareView in Slicer4 2011
Image:2011-01-24-Annotation.png| Slicer 4 Annotation Module 2011-01-24
Image:2011-01-24-Annotation.png| Slicer 4 Annotation Module 2011-01-24
Image:LiveUltrasoundModule-Slicer4.jpg| Slicer 4 Live ultrasound module for IGT spine procedures
Image:LiveUltrasoundModule-Slicer4_2.jpg| Slicer 4 Live ultrasound module for IGT prostate procedures
</gallery>

<gallery caption="2010" widths="200px" perrow="4">
Image:2010-SlicerAM QtAnnotation.png| Slicer 4 Annotation Module
Image:SlicerQT-2009-12-10.png|Slicer with Qt only
Image:QSlicerROIModule.png| ROI Module
</gallery>

File:UKFTractography CC.jpg

2014-01-09T22:52:16Z

Reckbo2:

Documentation/4.3/Modules/UKFTractography

2013-01-29T23:01:33Z

Reckbo2: Blanked the page

Documentation/4.3/Modules/UKFTractography

2013-01-29T22:59:18Z

Reckbo2: Created page with ' {{documentation/{{documentation/version}}/module-header}}   {{doc…'

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Yogesh Rathi, Ph.D, Psychiatry Neuroimaging Laboratory, Brigham & Women's Hospital 

Contact: Ryan Eckbo, <email>reckbo@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}} <- Replace this logo with yours
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}} <-Replace this logo with yours
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
We present a framework which uses an unscented Kalman filter for performing
tractography. At each point on the fiber the most consistent direction is found
as a mixture of previous estimates and of the local model.

It is very easy to expand the framework and to implement new fiber representations
for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor
methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion
ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be
identical) and the other one uses a full tensor representation.

Authors: Yogesh Rathi (yogesh@bwh.harvard.edu), Stefan Lienhard, Yinpeng Li, Martin
Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner (c.f.baumgartner@gmail.com),
Ryan Eckbo




{{documentation/{{documentation/version}}/module-section|Use Cases}}
* 1-Tensor tractography
* 1-Tensor tractography with free water
* 2-Tensor tractography
* 2-Tensor tractography with free water


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


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

Input/Output (IO)

--dwiFile <std::string> Input DWI Image

--seedsFile <std::string> Seeds for diffusion. If not specified, full brain tractography will be performed, and the algorithm will start from every voxel in the brain mask where the Generalized Anisotropy is bigger than 0.18

--labels <std::vector<int>> A vector of the ROI labels to be used (default: 1)

--maskFile <std::string> Mask for diffusion tractography

--tracts <std::string> Tracts generated, with first tensor output

--tractsWithSecondTensor <std::string> Tracts generated with second tensor output (if there is one)

Seeding Options

--seedsPerVoxel <int> Number of seeds per voxel (default: 1)

--seedFALimit<double> Seed points whose FA are below this value are excluded (default: 0.15)

Model Options

--numTensor <1|2|3> Number of tensors used (default: 2)

--fullTensorModel Whether to use the full tensor model. Which models all three eigenvalues seperately, as opposed to lambda2=lambda3.

--freeWater Adds a term for free water difusion to the model. If checked, the 1T simple model is forced.

Stopping Criteria

--minFA <double> Abort the tractography when the Fractional Anisotropy is less than this value (default: 0.15)

--minGA <double> Abort the tractography when the Generalized Anisotropy is less than this value (default: 0.1)

Fiber Scalar Fields

--recordFA Whether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor case to fiber.

--recordNMSE Whether to store NMSE. Attaches field 'NMSE' to fiber.

--recordTrace Whether to store Trace. Attaches field 'Trace', and 'Trace2' for 2-tensor case to fiber.

--recordFreeWater Whether to store the fraction of free water. Attaches field 'FreeWater' to fiber.

--recordState Whether to attach the states to the fiber. Will generate field 'state'.

--recordCovariance Whether to store the covariance. Will generate field 'covariance' in fiber.

--recordTensors Recording the tensors enables Slicer to color the fiber bundles by FA, orientation, and so on. The fields will be called 'TensorN', where N is the tensor number.

Advanced Options

--numThreads <int> Number of threads used during compuation. Set to the number of cores on your workstation for optimal speed. If left undefined boost will figure out the number of cores, and hence threads, during runtime.

--normalizedDWIData Whether the DWI input data is already normalized

--weightsOnTensors <std::vector<double>> Weights on different tensors when using multiple tensors. There must be one weight for each tensor, and the weights must sum up to 1. Defaults to equally weighted.

--maxHalfFiberLength <double> The max length limit of the half fibers generated during tractography. Here the fiber is "half" because the tractography goes in only one direction from one seed point at a time (default: 10000)

--Qm <double> Process noise for angles/direction (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).

--Ql <double> Process noise for eigenvalues (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).

--Qw <double> Process noise for free water weights, ignored if no free water estimation (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).

--Rs <double> Measurement noise (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).

--stepLength <double> Step length i.e. size of the step taken in the most consistent direction during each iteration of tractography given in millimeters (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).

--maxBranchingAngle <double> Maximum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between
(minBranchingAngle, maxBranchingAngle). Branching is supressed when this maxBranchingAngle is set to 0.0

--minBranchingAngle <double> Minimum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle)

Additional Output Options

--noTransformPosition Don't transform Points back from ijk->RAS when writing the output fiber

--branchesOnly Only output branches, ignore the primary tracts

--storeGlyphs Store tensors' main directions as two-point lines in a separate file named glyphs_{tracts}. When using multiple tensors, only the major tensors' main directions are stored

--outputNormalizedDWIData Whether to output the DWI after normalization (i.e. preprocessing)

Tractography unrelated options

--returnparameterfile <std::string> Filename in which to write simple return parameters (int, float, int-vector, etc.) as opposed to bulk return parameters (image, geometry, transform, measurement, table).

--processinformationaddress <std::string> Address of a structure to store process information (progress, abort, etc.). (default: 0)

--xml Produce xml description of command line arguments.

--echo Echo the command line arguments.

--, --ignore_rest Ignores the rest of the labeled arguments following this flag.

--version Displays version information and exits.

-h, --help Displays usage information and exits.




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


{{documentation/{{documentation/version}}/module-section|References}}
Reference for 2-tensor tractography:
* http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water:
* C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.


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


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

Documentation/Nightly/Modules/UKFTractography

2013-01-29T15:05:39Z

Reckbo2: Redirected page to Documentation/4.2/Modules/UKFTractography

#REDIRECT [[Documentation/4.2/Modules/UKFTractography]]

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

Documentation/4.2/Extensions/UKFTractography

2013-01-29T15:03:09Z

Reckbo2: Redirected page to Documentation/Nightly/Modules/UKFTractography

#REDIRECT [[Documentation/Nightly/Modules/UKFTractography]]

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

Documentation/4.2/Extensions

2013-01-29T15:01:04Z

Reckbo2: /* Cat 2 */

<noinclude>{{:{{FULLPAGENAME}}/Description}}

__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|CARMA]] (Alan Morris)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
** [[Documentation/{{documentation/version}}/Extensions/LabelToDICOMSEGImport|LabelToDICOMSEGConverter]]
** [[Documentation/{{documentation/version}}/Extensions/DICOMSEGImport|DICOM SEG Import]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|IGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylaward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]]

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

Documentation/Nightly/Modules/UKFTractography

2013-01-28T19:20:07Z

Reckbo2: Redirected page to Documentation/Nightly/Modules/UKFTractography

#REDIRECT [[Documentation/Nightly/Modules/UKFTractography]]

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

Documentation/Nightly/Modules

2013-01-28T19:18:55Z

Reckbo2: /* Diffusion */

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

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)

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

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/VolumeResliceDriver| Volume Reslice Driver]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)
[[image:UnderConstruction.png|tumb|10px]]

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

==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

Documentation/Nightly/Modules

2013-01-28T19:16:57Z

Reckbo2: /* Diffusion */

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

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)

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

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|Tractography UKF Tractography]]
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/VolumeResliceDriver| Volume Reslice Driver]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)
[[image:UnderConstruction.png|tumb|10px]]

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

==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

Documentation/Nightly/Extensions/UKFTractography

2013-01-28T19:13:11Z

Reckbo2: Redirected page to Documentation/Nightly/Modules/UKFTractography

#REDIRECT [[Documentation/Nightly/Modules/UKFTractography]]

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

Documentation/4.2/Modules/UKFTractography

2013-01-28T16:43:43Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-28T16:43:18Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-28T16:42:20Z

Reckbo2:

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Yogesh Rathi, Ph.D, Psychiatry Neuroimaging Laboratory, Brigham & Women's Hospital 

Contact: Ryan Eckbo, <email>reckbo@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}} <- Replace this logo with yours
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}} <-Replace this logo with yours
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
We present a framework which uses an unscented Kalman filter for performing
tractography. At each point on the fiber the most consistent direction is found
as a mixture of previous estimates and of the local model.

It is very easy to expand the framework and to implement new fiber representations
for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor
methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion
ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be
identical) and the other one uses a full tensor representation.

Authors: Yogesh Rathi (yogesh@bwh.harvard.edu), Stefan Lienhard, Yinpeng Li, Martin
Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner (c.f.baumgartner@gmail.com),
Ryan Eckbo




{{documentation/{{documentation/version}}/module-section|Use Cases}}
* 1-Tensor tractography
* 1-Tensor tractography with free water
* 2-Tensor tractography
* 2-Tensor tractography with free water


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


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

Input/Output (IO)

--dwiFile <std::string> Input DWI Image

--seedsFile <std::string> Seeds for diffusion. If not specified, full brain tractography will be performed, and the algorithm will start from every voxel in the brain mask where the Generalized Anisotropy is bigger than 0.18

--labels <std::vector<int>> A vector of the ROI labels to be used (default: 1)

--maskFile <std::string> Mask for diffusion tractography

--tracts <std::string> Tracts generated, with first tensor output

--tractsWithSecondTensor <std::string> Tracts generated with second tensor output (if there is one)

Seeding Options

--seedsPerVoxel <int> Number of seeds per voxel (default: 1)

--seedFALimit<double> Seed points whose FA are below this value are excluded (default: 0.15)

Model Options

--numTensor <1|2|3> Number of tensors used (default: 2)

--fullTensorModel Whether to use the full tensor model. Which models all three eigenvalues seperately, as opposed to lambda2=lambda3.

--freeWater Adds a term for free water difusion to the model. If checked, the 1T simple model is forced.

Stopping Criteria

--minFA <double> Abort the tractography when the Fractional Anisotropy is less than this value (default: 0.15)

--minGA <double> Abort the tractography when the Generalized Anisotropy is less than this value (default: 0.1)

Fiber Scalar Fields
--recordFA Whether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor case to fiber.
--recordNMSE Whether to store NMSE. Attaches field 'NMSE' to fiber.
--recordTrace Whether to store Trace. Attaches field 'Trace', and 'Trace2' for 2-tensor case to fiber.
--recordFreeWater Whether to store the fraction of free water. Attaches field 'FreeWater' to fiber.
--recordState Whether to attach the states to the fiber. Will generate field 'state'.
--recordCovariance Whether to store the covariance. Will generate field 'covariance' in fiber.
--recordTensors Recording the tensors enables Slicer to color the fiber bundles by FA, orientation, and so on. The fields will be called 'TensorN', where N is the tensor number.

Advanced Options
--numThreads <int> Number of threads used during compuation. Set to the number of cores on your workstation for optimal speed. If left undefined boost will figure out the number of cores, and hence threads, during runtime.
--normalizedDWIData Whether the DWI input data is already normalized
--weightsOnTensors <std::vector<double>> Weights on different tensors when using multiple tensors. There must be one weight for each tensor, and the weights must sum up to 1. Defaults to equally weighted.
--maxHalfFiberLength <double> The max length limit of the half fibers generated during tractography. Here the fiber is "half" because the tractography goes in only one direction from one seed point at a time (default: 10000)
--Qm <double> Process noise for angles/direction (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Ql <double> Process noise for eigenvalues (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Qw <double> Process noise for free water weights, ignored if no free water estimation (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Rs <double> Measurement noise (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--stepLength <double> Step length i.e. size of the step taken in the most consistent direction during each iteration of tractography given in millimeters (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--maxBranchingAngle <double> Maximum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle). Branching is supressed when this maxBranchingAngle is set to 0.0
--minBranchingAngle <double> Minimum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle)

Additional Output Options
--noTransformPosition Don't transform Points back from ijk->RAS when writing the output fiber
--branchesOnly Only output branches, ignore the primary tracts
--storeGlyphs Store tensors' main directions as two-point lines in a separate file named glyphs_{tracts}. When using multiple tensors, only the major tensors' main directions are stored
--outputNormalizedDWIData Whether to output the DWI after normalization (i.e. preprocessing)

Tractography unrelated options
--returnparameterfile <std::string> Filename in which to write simple return parameters (int, float, int-vector, etc.) as opposed to bulk return parameters (image, geometry, transform, measurement, table).
--processinformationaddress <std::string> Address of a structure to store process information (progress, abort, etc.). (default: 0)
--xml Produce xml description of command line arguments.
--echo Echo the command line arguments.
--, --ignore_rest Ignores the rest of the labeled arguments following this flag.
--version Displays version information and exits.
-h, --help Displays usage information and exits.




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


{{documentation/{{documentation/version}}/module-section|References}}
Reference for 2-tensor tractography:
* http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water:
* C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.


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


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

Documentation/4.2/Modules/UKFTractography

2013-01-28T16:41:27Z

Reckbo2:

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Yogesh Rathi, Ph.D, Psychiatry Neuroimaging Laboratory, Brigham & Women's Hospital 

Contact: Ryan Eckbo, <email>reckbo@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}} <- Replace this logo with yours
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}} <-Replace this logo with yours
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
We present a framework which uses an unscented Kalman filter for performing
tractography. At each point on the fiber the most consistent direction is found
as a mixture of previous estimates and of the local model.

It is very easy to expand the framework and to implement new fiber representations
for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor
methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion
ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be
identical) and the other one uses a full tensor representation.

Authors: Yogesh Rathi (yogesh@bwh.harvard.edu), Stefan Lienhard, Yinpeng Li, Martin
Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner (c.f.baumgartner@gmail.com),
Ryan Eckbo




{{documentation/{{documentation/version}}/module-section|Use Cases}}
* 1-Tensor tractography
* 1-Tensor tractography with free water
* 2-Tensor tractography
* 2-Tensor tractography with free water


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


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
Input/Output (IO)
--dwiFile <std::string> Input DWI Image

--seedsFile <std::string> Seeds for diffusion. If not specified, full brain tractography will be performed, and the algorithm will start from every voxel in the brain mask where the Generalized Anisotropy is bigger than 0.18
--labels <std::vector<int>> A vector of the ROI labels to be used (default: 1)
--maskFile <std::string> Mask for diffusion tractography
--tracts <std::string> Tracts generated, with first tensor output
--tractsWithSecondTensor <std::string> Tracts generated with second tensor output (if there is one)

Seeding Options
--seedsPerVoxel <int> Number of seeds per voxel (default: 1)
--seedFALimit<double> Seed points whose FA are below this value are excluded (default: 0.15)

Model Options
--numTensor <1|2|3> Number of tensors used (default: 2)
--fullTensorModel Whether to use the full tensor model. Which models all three eigenvalues seperately, as opposed to lambda2=lambda3.
--freeWater Adds a term for free water difusion to the model. If checked, the 1T simple model is forced.

Stopping Criteria
--minFA <double> Abort the tractography when the Fractional Anisotropy is less than this value (default: 0.15)
--minGA <double> Abort the tractography when the Generalized Anisotropy is less than this value (default: 0.1)

Fiber Scalar Fields
--recordFA Whether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor case to fiber.
--recordNMSE Whether to store NMSE. Attaches field 'NMSE' to fiber.
--recordTrace Whether to store Trace. Attaches field 'Trace', and 'Trace2' for 2-tensor case to fiber.
--recordFreeWater Whether to store the fraction of free water. Attaches field 'FreeWater' to fiber.
--recordState Whether to attach the states to the fiber. Will generate field 'state'.
--recordCovariance Whether to store the covariance. Will generate field 'covariance' in fiber.
--recordTensors Recording the tensors enables Slicer to color the fiber bundles by FA, orientation, and so on. The fields will be called 'TensorN', where N is the tensor number.

Advanced Options
--numThreads <int> Number of threads used during compuation. Set to the number of cores on your workstation for optimal speed. If left undefined boost will figure out the number of cores, and hence threads, during runtime.
--normalizedDWIData Whether the DWI input data is already normalized
--weightsOnTensors <std::vector<double>> Weights on different tensors when using multiple tensors. There must be one weight for each tensor, and the weights must sum up to 1. Defaults to equally weighted.
--maxHalfFiberLength <double> The max length limit of the half fibers generated during tractography. Here the fiber is "half" because the tractography goes in only one direction from one seed point at a time (default: 10000)
--Qm <double> Process noise for angles/direction (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Ql <double> Process noise for eigenvalues (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Qw <double> Process noise for free water weights, ignored if no free water estimation (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Rs <double> Measurement noise (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--stepLength <double> Step length i.e. size of the step taken in the most consistent direction during each iteration of tractography given in millimeters (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--maxBranchingAngle <double> Maximum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle). Branching is supressed when this maxBranchingAngle is set to 0.0
--minBranchingAngle <double> Minimum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle)

Additional Output Options
--noTransformPosition Don't transform Points back from ijk->RAS when writing the output fiber
--branchesOnly Only output branches, ignore the primary tracts
--storeGlyphs Store tensors' main directions as two-point lines in a separate file named glyphs_{tracts}. When using multiple tensors, only the major tensors' main directions are stored
--outputNormalizedDWIData Whether to output the DWI after normalization (i.e. preprocessing)

Tractography unrelated options
--returnparameterfile <std::string> Filename in which to write simple return parameters (int, float, int-vector, etc.) as opposed to bulk return parameters (image, geometry, transform, measurement, table).
--processinformationaddress <std::string> Address of a structure to store process information (progress, abort, etc.). (default: 0)
--xml Produce xml description of command line arguments.
--echo Echo the command line arguments.
--, --ignore_rest Ignores the rest of the labeled arguments following this flag.
--version Displays version information and exits.
-h, --help Displays usage information and exits.




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


{{documentation/{{documentation/version}}/module-section|References}}
Reference for 2-tensor tractography:
* http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water:
* C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.


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


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

Documentation/4.2/Modules/UKFTractography

2013-01-28T16:41:05Z

Reckbo2:

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Yogesh Rathi, Ph.D, Psychiatry Neuroimaging Laboratory, Brigham & Women's Hospital 

Contact: Ryan Eckbo, <email>reckbo@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}} <- Replace this logo with yours
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}} <-Replace this logo with yours
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
We present a framework which uses an unscented Kalman filter for performing
tractography. At each point on the fiber the most consistent direction is found
as a mixture of previous estimates and of the local model.

It is very easy to expand the framework and to implement new fiber representations
for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor
methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion
ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be
identical) and the other one uses a full tensor representation.

Authors: Yogesh Rathi (yogesh@bwh.harvard.edu), Stefan Lienhard, Yinpeng Li, Martin
Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner (c.f.baumgartner@gmail.com),
Ryan Eckbo




{{documentation/{{documentation/version}}/module-section|Use Cases}}
* 1-Tensor tractography
* 1-Tensor tractography with free water
* 2-Tensor tractography
* 2-Tensor tractography with free water


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


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
Input/Output (IO)
--dwiFile <std::string> Input DWI Image
--seedsFile <std::string> Seeds for diffusion. If not specified, full brain tractography will be performed, and the algorithm will start from every voxel in the brain mask where the Generalized Anisotropy is bigger than 0.18
--labels <std::vector<int>> A vector of the ROI labels to be used (default: 1)
--maskFile <std::string> Mask for diffusion tractography
--tracts <std::string> Tracts generated, with first tensor output
--tractsWithSecondTensor <std::string> Tracts generated with second tensor output (if there is one)

Seeding Options
--seedsPerVoxel <int> Number of seeds per voxel (default: 1)
--seedFALimit<double> Seed points whose FA are below this value are excluded (default: 0.15)

Model Options
--numTensor <1|2|3> Number of tensors used (default: 2)
--fullTensorModel Whether to use the full tensor model. Which models all three eigenvalues seperately, as opposed to lambda2=lambda3.
--freeWater Adds a term for free water difusion to the model. If checked, the 1T simple model is forced.

Stopping Criteria
--minFA <double> Abort the tractography when the Fractional Anisotropy is less than this value (default: 0.15)
--minGA <double> Abort the tractography when the Generalized Anisotropy is less than this value (default: 0.1)

Fiber Scalar Fields
--recordFA Whether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor case to fiber.
--recordNMSE Whether to store NMSE. Attaches field 'NMSE' to fiber.
--recordTrace Whether to store Trace. Attaches field 'Trace', and 'Trace2' for 2-tensor case to fiber.
--recordFreeWater Whether to store the fraction of free water. Attaches field 'FreeWater' to fiber.
--recordState Whether to attach the states to the fiber. Will generate field 'state'.
--recordCovariance Whether to store the covariance. Will generate field 'covariance' in fiber.
--recordTensors Recording the tensors enables Slicer to color the fiber bundles by FA, orientation, and so on. The fields will be called 'TensorN', where N is the tensor number.

Advanced Options
--numThreads <int> Number of threads used during compuation. Set to the number of cores on your workstation for optimal speed. If left undefined boost will figure out the number of cores, and hence threads, during runtime.
--normalizedDWIData Whether the DWI input data is already normalized
--weightsOnTensors <std::vector<double>> Weights on different tensors when using multiple tensors. There must be one weight for each tensor, and the weights must sum up to 1. Defaults to equally weighted.
--maxHalfFiberLength <double> The max length limit of the half fibers generated during tractography. Here the fiber is "half" because the tractography goes in only one direction from one seed point at a time (default: 10000)
--Qm <double> Process noise for angles/direction (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Ql <double> Process noise for eigenvalues (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Qw <double> Process noise for free water weights, ignored if no free water estimation (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--Rs <double> Measurement noise (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--stepLength <double> Step length i.e. size of the step taken in the most consistent direction during each iteration of tractography given in millimeters (Will be set during runtime to the optimal value for the chosen model, unless overriden by user).
--maxBranchingAngle <double> Maximum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle). Branching is supressed when this maxBranchingAngle is set to 0.0
--minBranchingAngle <double> Minimum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors' major directions form an angle between (minBranchingAngle, maxBranchingAngle)

Additional Output Options
--noTransformPosition Don't transform Points back from ijk->RAS when writing the output fiber
--branchesOnly Only output branches, ignore the primary tracts
--storeGlyphs Store tensors' main directions as two-point lines in a separate file named glyphs_{tracts}. When using multiple tensors, only the major tensors' main directions are stored
--outputNormalizedDWIData Whether to output the DWI after normalization (i.e. preprocessing)

Tractography unrelated options
--returnparameterfile <std::string> Filename in which to write simple return parameters (int, float, int-vector, etc.) as opposed to bulk return parameters (image, geometry, transform, measurement, table).
--processinformationaddress <std::string> Address of a structure to store process information (progress, abort, etc.). (default: 0)
--xml Produce xml description of command line arguments.
--echo Echo the command line arguments.
--, --ignore_rest Ignores the rest of the labeled arguments following this flag.
--version Displays version information and exits.
-h, --help Displays usage information and exits.




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


{{documentation/{{documentation/version}}/module-section|References}}
Reference for 2-tensor tractography:
* http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water:
* C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
on computational diffusion MRI, 2012.


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


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

Documentation/4.2/Modules/UKFTractography

2013-01-26T19:29:55Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-26T19:27:21Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-26T19:26:50Z

Reckbo2:

Documentation/Nightly/Modules/YOURMODULENAME

2013-01-26T19:23:55Z

Reckbo2:

Documentation/Nightly/Modules/YOURMODULENAME

2013-01-26T19:21:27Z

Reckbo2: Undo revision 29994 by Reckbo2 (Talk)

Documentation/Nightly/Modules/YOURMODULENAME

2013-01-26T18:43:44Z

Reckbo2:

Documentation/Nightly/Modules/YOURMODULENAME

2013-01-26T18:42:03Z

Reckbo2:

Documentation/Nightly/Modules/YOURMODULENAME

2013-01-26T18:39:56Z

Reckbo2:

Documentation/Nightly/Modules/YOURMODULENAME

2013-01-26T18:39:30Z

Reckbo2:

Documentation/Nightly/Modules/YOURMODULENAME

2013-01-26T18:38:59Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-26T18:37:45Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-26T18:36:45Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-26T18:36:31Z

Reckbo2:

Documentation/4.2/Modules/UKFTractography

2013-01-26T18:34:49Z

Documentation/4.2/Modules

2013-01-26T18:33:41Z

Reckbo2: /* Diffusion */

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

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)

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

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKFTractography]][[image:UnderConstruction.png|tumb|10px]]
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/VolumeResliceDriver| Volume Reslice Driver]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)

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

==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

Documentation/4.2/Modules

2013-01-26T18:33:21Z

Reckbo2: /* Diffusion */

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

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)

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

==Registration==
*[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)
*[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)
*[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)

==Segmentation==
*[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan)
*Specialized
**[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)
**[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)
**[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)
* Change quantification
** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman)
*Utilities
**[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman)
**[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Data Conversion
**[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)
**[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKFTractography]][[image:UnderConstruction.png|tumb|10px]]

==IGT==
*[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/VolumeResliceDriver| Volume Reslice Driver]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]

==Filtering==
*[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin)
**[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)
**[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin)
*[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]

==Converters==
*[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller)
*[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper)

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

==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==
* MultiVolume Support
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)
**[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)

==Developer Tools==
*[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)
*Performance Tests
*Tractography

==Legacy==
*Converters
**[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]
*Diffusion
**Denoising
***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]
*Filtering
**[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Registration
**[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]

*Segmentation
**[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

Modules:StochasticTractography-Documentation-3.6

2011-10-19T19:52:14Z

Reckbo2:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
__NOTOC__
===Module Name===
Stochastic Tractography

{|
|[[Image:Cc_01.png|thumb|280px|Corpus callosum with stochastic tractography]]
|[[Image:Cc_stoch.png|thumb|280px|Corpus callosum lateral projections]]
|}

== General Information ==

This module is no longer maintained.

===Module Type & Category===

Type: Interactive

Category: DTI

===Authors, Collaborators & Contact===
* Author: Julien von Siebenthal
* Contributor: Steve Pieper
* Contact: Ryan Eckbo, PNL, reckbo at bwh.harvard.edu

===Module Description===
As a main purpose, the stochastic tractography module helps to evaluate connectivity between two regions of interest (ROIs) of the brain. These ROIs define generally grey matter regions having a specific neurophysiological function. Extensively, study involving more than two regions could still be done by pairing the regions two by two.

To go deeper into learning the module you can download the following [http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial tutorial]

== Usage ==
* You want to study fiber path from a single region of interest (ROI)
* You want to evaluate connectivity between two ROIs

=== Description ===

{|
|[[Image:General.png|thumb|1000px|Stochastic tractography panel]]
|}

With the stochastic tractography module, you can:
{|
|
* Feature 1 : smooth the given Diffusion Weighted Image (DWI) using a Half Width Full Maximum gaussian filter
{|
|[[Image:smooth2.png|thumb|500px|Smoothing step]]
|}
|}

{|
|
* Feature 2 : generate a brain mask from the DWI baseline input
{|
|[[Image:mask2.png|thumb|500px|Brain mask step]]
|}
|}

{|
|
* Feature 3 : create a DTI (Diffusion Tensor Image) tensor from the DWI input
{|
|[[Image:tensor2.png|thumb|500px|Tensor step]]
|}
|}

{|
|
* Feature 4 : produce different measures based on the tensor like fractional anistropy (FA), mode and trace
{|
|[[Image:fa2.png|thumb|500px|Tensor step: FA]]
|[[Image:mode2.png|thumb|500px|Tensor step: mode]]
|[[Image:trace2.png|thumb|500px|Tensor step: trace]]
|}
|}

{|
|
* Feature 5 : produce connection maps in case 2 ROIs are given without ROI filtering from the tractography
** showing union and intersection of both maps from region A to region B and B to A
{|
|[[Image:AorB2.png|thumb|500px|Union of A to B and B to A]]
|[[Image:AandB2.png|thumb|500px|Intersection of A to B and B to A]]
|}
|}

{|
|
* Feature 6 : produce connection maps in case 2 ROIs are given with ROI filtering from the tractography
** showing only tracts connecting region A to region B and B to A
{|
|[[Image:connectAB2.png|thumb|500px|ROI filtering]]
|[[Image:A2B2.png|thumb|500px|ROI filtering from A to B]]
|[[Image:B2A2.png|thumb|500px|ROI filtering from B to A]]
|}
|}

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

{|
|
* '''IO panel:'''
** Input DWI Volume: the DWI is loaded through the Volume module - it is th only mandatory input
** Input ROI Volume (A/B): only 1 ROI is needed to achieve a tractography. If you want to evaluate the connection between two regions, you will give both ROIs
** Input WM Volume: a white matter mask can be given as input to use ones provided by other tools or Slicer modules - it will supersede the brain mask even if enabled. Be mindful in setting a WM: tractography results can be impaired by a too restrictive WM
** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 features just require a DWI
{|
|[[Image:IOmenu.png|thumb|500px|IO step]]
|}
|}

{|
|
* '''Smoothing panel:'''
** Gaussian FWHM: this filter defines a Full Width Half Maximum. You can define it for each direction in modifying each component of the 3-vector
** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
{|
|[[Image:Smoothmenu.png|thumb|500px|Smoothing step]]
|}
|}

{|
|
* '''Brain Mask panel:'''
** Lower/Higher Brain Threshold: this filter is based on a simple level set segmentation - intensities of the baseline lying between the two values will be represented, others are set to 0. The most common use of this filter is to remove ventricles from the tractography domain and most of the outside of the brain
** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
{|
|[[Image:Maskmenu.png|thumb|500px|Brain mask step]]
|}
|}

{|
|
* '''Diffusion Tensor panel:'''
** Important: this step is not mandatory. It is here to evaluate the whole tensor and achieve measurements like FA, mode or trace. You did not need it to achieve tractography
** FA, mode and trace are sent as scalar volumes and inserted in the MRML tree to be further used
** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
{|
|[[Image:Tensormenu.png|thumb|500px|Tensor step]]
|}
|}

{|
|
* '''Tractography panel:''' This panel deals with the tractography per se:
** Total tracts: number of generated tracts per voxel
** Maximum tract length (mm): set the maximum length a tract could reach
** Step size (mm): is the step length for the update vector
** Use spacing: must be used with caution - activate spacing of the update vector
** Stopping criteria: FA is used as the stopping criteria. Advice: as ROIs are defined in the grey matter FA are generally very low, therefore do not use it in most cases
{|
|[[Image:Tractomenu.png|thumb|500px|Tractography step]]
|}
|}

{|
|
* '''Connectivity Map panel:''' This panel lets the user modify parameters to create density/connectivity maps. A map is a scalar volume storing the number of times each voxel is traversed by tracts. It can be counted differently which is the purpose of the following parameters:
** Computation mode:
*** binary: voxel counter is incremented by 1 only once
*** cumulative: voxel counter is incremented by 1 each time a tract traverses it
*** weighted: same as cumulative but the increment is the length of the tract traversing the voxel
** Length based: must be enabled if the resulting tracts must be subdivided related to their length ownership
*** dThird: tracts only counted have length between 1 and (maximum tract length)/3
*** mThird: tracts only counted have length between (maximum tract length)/3 and 2 * (maximum tract length)/3
*** uThird: tracts only counted have length between 2 * (maximum tract length)/3 and (maximum tract length)
*** vicinity: in case of 2 ROIs connectivity assessment, setting vicinity to a positive value creates a neighborhood (in voxels) around the ROIs. This could help in counting tracts that ternminate near the ROIs but not accurately in
*** threshold: defines the connection probability under which tracts are rejected
{|
|[[Image:Connectmenu.png|thumb|500px|Connectivity step]]
|}
|}

== Development ==

===Dependencies===

Volumes

===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===

== More Information ==

===Acknowledgment===
National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (to Ron Kikinis, Marek Kubicki).

===References===
* [http://lmi.bwh.harvard.edu/papers/pdfs/2002/bjornemoMICCAI02.pdf Björnemo M, Brun A, Kikinis R, Westin CF. Regularized stochastic white matter tractography using diffusion tensor MRI. In Fifth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'02). Tokyo, Japan, 2002;435-442.]
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]