=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4

=Jan 2011=
*Outline of plans

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

Port the fiducial tractography seeding to new infrastructure (Alex)

Port tensor estimation tools

Implement quick and fluid exploration of pre-calculated full-brain tractographies (Demain?)

Cluster interactive exploration, cluster labeling (Lauren)

Fiber laterality module (Lauren)

*Schedule until June
Meet weekly on Tuesdays
Feb 1, Discuss overall plan
Feb 8, Define new infrastructure to allow efficient tractography
Feb 15, Define new infrastructure to allow efficient tractography
Feb 22, Discuss user-interface work flow

Deliverables Feb: Solid plan March

Mar 1
Mar 8
Mar 15
Mar 22
Mar 29

Deliverables Mar: Interactive tractography

April 5
April 12
April 19
April 26

Deliverables April

May 3
May 10
May17
May 24
May 31

Deliverable May:

June: debug, test

June (AHM),

Slicer4:Diffusion

2011-01-28T22:36:35Z

Westin: /* Jan 2011 */

Slicer4:Diffusion

2011-01-28T22:32:53Z

Westin: /* Jan 2011 */

=Introduction=
This page contains descriptions and plans for the dMRI framework in Slicer 4

=Jan 2011=
*Outline of plans

Port the fiducial tractography seeding to new infrastructure

Quick and fluid exploration of full-brain tractographies

*Schedule until June

Announcements:Slicer3.6

2010-06-23T17:35:02Z

Westin: /* Introduction */

[[Documentation-3.6|Back to Documentation 3.6]]
[[image:Slicer3-6Announcement-v2.png|3.6 Icon large]]

=Introduction=

The [[Announcments-3.6-Team|community]] of Slicer developers is proud to announce the release of '''Slicer 3.6'''.

*Click here to [http://www.slicer.org/pages/Downloads download] different versions of Slicer3 and find pointers to the source code, mailing lists and bug tracker. *Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer3 are not fully tested.
*The [[Training|Slicer Training page]] provides a series of courses for learning how to use Slicer3. The portfolio contains self-guided presentation and sample data sets

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

=Our Philosophy=
Slicer is a community platform created for the purpose of subject specific image analysis and visualization.

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

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

=Slicer Highlights=
<gallery caption="Slicer v3.6 - New and Improved Modules" widths="250px" heights="150px" perrow="3">
Image:Slicer3.6-Editor-2010-05-06.png|The [[Modules:Editor-Documentation-3.6|Interactive Editor]] can be used to create and edit label maps for quantitative analysis and surface model generation (Steve Pieper)
Image:VolumeRenderingICPE.png| [[Modules:VolumeRendering-Documentation-3.6|Volume Rendering]] (Yanling Liu, Julien Finet, Lisa Avila)
Image:Slicer-ColorGUI-3.6.jpg| [[Modules:Colors-Documentation-3.6|Colors]] (Nicole Aucoin)
Image:Slicer3.6MeasurementsRulersModel.jpg| [[Modules:Measurements-Documentation-3.6 |Measurements (rulers and angles)]] (Nicole Aucoin)
Image:SlicerFiducialsGlyphs-3.4.jpg| [[Modules:Fiducials-Documentation-3.6|Fiducials]] (Nicole Aucoin)
Image:EMSegment-Simple.png|[[Modules:EMSegment-Simple3.6|EM Segmenter, simple version]] (Kilian Pohl)
Image:Fastmarching-result-adjusted.jpg| [[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
Image:RSSkidneyL.png| [[Modules:RobustStatisticsSeg-Documentation-3.6|Robust Statistical Segmentation]] (Yi Gao)
Image:Fiducial registration before.jpg|NEW: [[Modules:RegisterImagesMultiRes-Documentation-3.6|Multiresolution Affine registration]] (Casey Goodlett)
Image:B-spline-reg-detail.png|Improved: [[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]] (Casey Goodlett)
Image:Fiducial_registration_before.jpg|NEW: [[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]] (Casey Goodlett)
Image:Registration_BRAINSfit.png|NEW: [[Modules:BRAINSFit |BRAINSFit Registration]] (Hans Johnson)
Image:Registration_BRAINSdemonwarp.png|NEW: [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] (Hans Johnson)
Image:BRAINSResample.png|NEW: [[Modules:BRAINSResample|BRAINSResample]] (Hans J. Johnson)
Image:BRAINSROIAuto.png|NEW: [[Modules:BRAINSROIAuto|BRAINSROIAuto]] (Hans J. Johnson)
Image:Plastimatch_icon.png|NEW: [[Modules:Plastimatch |Plastimatch non-rigid registration]] (Greg Sharp)
Image:PETCTFusion.png| [[Modules:PETCTFusion-Documentation-3.6 |PETCTFusion]] (Wendy Plesniak)
Image:| [[Modules:CollectFiducials-Documentation-3.6 |Collect Patient Fiducials]] (Andrew Wiles)
Image:| [[Modules:IGTToolSelector-Documentation-3.6 |IGT Tool Selector]] (Andrew Wiles)
Image:FourDImage Screenshot1.png| [[Modules:FourDImage-Documentation-3.6|4D Image Viewer]] (Junichi Tokuda)
Image:MRI_Bias_Field_Correction_Slicer3_close_up.png|[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRIBiasFieldCorrection]] correction of MRI intensity inhomogeneity i.e. bias field (Sylvain Jaume)
Image:N4 prostate bias ax.png| [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)
Image:Surface H c.png| [[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
Image:ModelTransform.PNG| [[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)
Image:BrainWebImageTransformed.jpg| [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
Image:ExtractSubvolume3.png| [[Modules:CropVolume-Documentation-3.6|Crop Volume]] (Andriy Fedorov)
Image:Endoscopy-slicer3.6.png| [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)
Image:ChangeTracker_Analysis-3.4.png| [[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
Image:Slicer3_OpenIGTLinkIF__VolumeReslice2.png| [[Modules:OpenIGTLinkIF-Documentation-3.6|OpenIGTLinkIF]] (Junichi Tokuda)
Image:ProstateNav-3.6_Transrectal.png| [[Modules:ProstateNav-Documentation-3.6|ProstateNav]] (Andras Lasso, Junichi Tokuda)
Image:slicer3.6_neuronav_OR.jpeg| [[Modules:NeuroNav-Documentation-3.6|NeuroNav]] (Haiying Liu)
Image:IGTToolSelectorPointer.png |[[Modules:IGTToolSelector-Documentation-3.6|IGT tool selector]] (A. Wiles)
</gallery>

=Slicer Extensions=
<gallery caption="Slicer v3.6 - Extensions" widths="250px" heights="150px" perrow="3">
Image:Plastimatch_dicomrt_dose.png|The [[Modules:PlastimatchDICOMRT| Plastimatch DICOM RT reader]] allows import and conversion of data in that format. (Greg Sharp)
Image:ABC out3d.png|The [[Modules:ABC-Documentation-3.5|ABC Segmenter]] is based on ITK EM technology.
Image:FCMResultLabels-3-6.png|[[Modules:FuzzySegmentationModule|Fuzzy segmentation]]
Image:HammerAverage-3-6.png|[[Modules:HammerRegistration|Hammer Registration]] can be used to build statistical brain atlases
Image:Plastimatch image 2.png|[[Modules:Plastimatch|Plastimatch non-rigid registration]] (Greg Sharp)
Image:Corticalthickness.png|[[Modules:ARCTIC-Documentation-3.6|Arctic wizard]] (Automatic Regional Cortical ThICkness)
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6| Lupus white matter lesions segmentation]] (Jeremy Bockholt, Mark Scully)
Image:Shot2.png|[[Modules:EMDTIClustering-Documentation-3.6|EM DTI clustering]] (Mahnaz Maddah)
Image:RicianTensorCorrectionImage.png|[[Modules:RicianNoiseFilter|Rician Noise Filter]] for noise removal in DWI data
Image:FourDAnalysisModuleScreenShot-3.5.png|The [[Modules:FourDAnalysis-Documentation-3.6|FourD Analysis module]] was designed for time series analysis (Junichi Takuda)
Image:Avf 3d voronoi big.png|[[Modules:VMTKCenterlines|Centerline extraction using Voronoi diagrams]] (Luca Antiga, Daniel Haehn)
Image:Labeldiameterestimation1.png|[[Modules:LabelDiameterEstimation-Documentation-3.6|Label diameter estimation]] (Andriy Fedorov)
</gallery>

Checklist for the [[Checklist-3.6-Release|3.6 release]]

= Other Improvements, Additions & Documentation =
<gallery caption="" widths="250px" heights="150px" perrow="3">
image:3.6 Default LUT.png| [[Slicer3:2010_GenericAnatomyColors|New default LUT]] (Michael Halle)
Image:RegPortal_Icon.png|[[Slicer3:Registration|Registration Portal Page: overview of avail. tools & modules]] (Dominik Meier)
Image:Resampling_DecisionMatrix.png|[[Registration:Resampling|Resampling Tool Feature Matrix]] (Dominik Meier)
Image:RegLib_Banner.png|[http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory Slicer Registration Case Library] (Dominik Meier)
Image:RegistrationWelcome_icon.png|[[Slicer3:Registration|Registration Welcome Module]] gives an overview of avail. registration modules
Image:SegmentationWelcome_icon.png|[[Modules:SegmentationOverview3.6|Segmentation Welcome Module]] gives an overview of avail. segmentation modules
Image:DiffusionWelcome_icon.png|[[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion Welcome Module]] gives an overview of avail. DWI processing modules
Image:ITK_logo.png|[http://www.kitware.com/news/home/browse/272 ITK upgrades] provided performance improvements in all registration modules and many other modules.
</gallery>

Modules:UnbiasedNonLocalMeans-Documentation-3.6

2010-05-17T08:30:20Z

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

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

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

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

Type: Interactive

Category: CLI/DiffusionApplications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega , Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the images using a Unbiased Non Local Means for Rician noise algorithm. It exploits not only the spatial redundancy, but the redundancy in similar gradient directions as well; it takes into account the N closest gradient directions to the direction being processed (a maximum of 5 gradient directions is allowed to keep a reasonable computational load, since we do not use neither similarity maps nor block-wise implementation).

The noise parameter is automatically estimated in the same way as in the jointLMMSE module.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

Please, note that the execution of this filter is extremely slow, son only very conservative parameters (block size and search size as small as possible) should be used. Even so, its execution may take several hours. The advantage of this filter over joint LMMSE is its better preservation of edges and fine structures.

== Usage ==

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

To use this filter, just load a DWI volume (gradient directions must be known) and apply the filter, as illustrated below. A brief summary of the parameters used is given below.

Before filtering:
{|
|[[Image:orig.png|thumb|600px|Original unfiltered image]]
|}

After filtering:
{|
|[[Image:UNLM.png|thumb|600px|Result after filtering with the unbiased non-local means method. This method performs relatively well, but has very high computational cost.]]
|}

===Quick Tour of Features and Use===
Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Search radius:''' This filter works by computing the weighted average of pixels in a large neighborhood. The search radius is the 3D radius of that neighborhood.
* '''Comparison radius:''' The weights of the average are computed as the negative exponential of the (normalized) distance between two neighborhoods which have a 3D radius of this size.
* '''h:''' The normalization constant for the distance between neighborhoods. This parameter is related to the noise power, and should be in the range 0.8->1.2. Higher values produce more blurring (and more noise reduction), while lower values better preserve edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. It is strongly recommended to keep this parameter less than 5 to keep a reasonable computational load. Even so, this filter is extremely slow.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

This filter is very slow. May take hours.

===Source code & documentation===
Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/dwiUNLM link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1UNLMFilter.html itkUNLMFilter.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:UnbiasedNonLocalMeans-Documentation-3.6

2010-05-17T08:29:12Z

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

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

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

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

Type: Interactive

Category: CLI/DiffusionApplications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega , Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the images using a Unbiased Non Local Means for Rician noise algorithm. It exploits not only the spatial redundancy, but the redundancy in similar gradient directions as well; it takes into account the N closest gradient directions to the direction being processed (a maximum of 5 gradient directions is allowed to keep a reasonable computational load, since we do not use neither similarity maps nor block-wise implementation).

The noise parameter is automatically estimated in the same way as in the jointLMMSE module.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

Please, note that the execution of this filter is extremely slow, son only very conservative parameters (block size and search size as small as possible) should be used. Even so, its execution may take several hours. The advantage of this filter over joint LMMSE is its better preservation of edges and fine structures.

== Usage ==

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

To use this filter, just load a DWI volume (gradient directions must be known) and apply the filter, as illustrated below. A brief summary of the parameters used is given below.

Before filtering:
{|
|[[Image:orig.png|thumb|600px|Original unfiltered image]]
|}

After filtering:
{|
|[[Image:UNLM.png|thumb|600px|Original unfiltered image]]
|}

===Quick Tour of Features and Use===
Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Search radius:''' This filter works by computing the weighted average of pixels in a large neighborhood. The search radius is the 3D radius of that neighborhood.
* '''Comparison radius:''' The weights of the average are computed as the negative exponential of the (normalized) distance between two neighborhoods which have a 3D radius of this size.
* '''h:''' The normalization constant for the distance between neighborhoods. This parameter is related to the noise power, and should be in the range 0.8->1.2. Higher values produce more blurring (and more noise reduction), while lower values better preserve edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. It is strongly recommended to keep this parameter less than 5 to keep a reasonable computational load. Even so, this filter is extremely slow.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

This filter is very slow. May take hours.

===Source code & documentation===
Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/dwiUNLM link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1UNLMFilter.html itkUNLMFilter.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:RicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:28:23Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. Images corresponding to each gradient direction, including baseline, are processed individually. The noise parameter is automatically estimated (noise estimation improved but slower).

Note that this is a general purpose filter for MRi images. The module jointLMMSE has been specifically designed for DWI volumes and shows a better performance, so its use is recommended instead.

A complete description of the algorithm in this module can be found in:

S. Aja-Fernández, M. Niethammer, M. Kubicki, M. Shenton, and C.-F. Westin. "Restoration of DWI data using a Rician LMMSE estimator". IEEE Transactions on Medical Imaging, 27(10): pp. 1389-1403, Oct. 2008.

== Usage ==

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

A brief description of the most important parameters is given below.

Before filtering:
{|
|[[Image:orig.png|thumb|600px|Original unfiltered image]]
|}

After filtering:

{|
|[[Image:LMMSE.png|thumb|600px|Original unfiltered image]]
|}

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===
Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/dwiNoiseFilter link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeStatisticsWherePositiveFilter.html itkComputeStatisticsWherePositiveFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ExtractVolumeFilter.html itkExtractVolumeFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilterStep.html itkLMMSEVectorImageFilterStep.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1MaskedMeanImageFilter.html itkMaskedMeanImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1VectorImageCastFilter.html itkVectorImageCastFilter.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

Modules:JointRicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:26:52Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.

The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

== Usage ==

The filter operates on an input DWI volume (gradient directions must be known). The meaning of the parameters of this module is listed below.

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

The following screenshots illustrate how to use the filter and the expected results (note that the optimal parameters strongly depends on the characteristics of the image: voxel size, number of gradients...).

Before filtering:

{|
|[[Image:Orig.png|thumb|600px|Original unfiltered image]]
|}

After filtering:

{|
|[[Image:jLMMSE.png|thumb|600px|Original unfiltered image]]
|}

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood. A large radius more effectively reduces the noise but may induce a certain blurring of the edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. If N=0 is fixed, then all gradient directions are filtered together.
** NOTE: If N=1 is used this filter is similar (but not equal) to RicianLMMSEImageFilter. Two main differences exist: 1) 4-th order moments have to be computed only for baseline(s) image(s), and 2) if more than one baseline is present all of them are filtered together even if N=1.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===

Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/jointLMMSE link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:JointRicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:26:11Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.

The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

== Usage ==

The filter operates on an input DWI volume (gradient directions must be known). The meaning of the parameters of this module is listed below.

===Examples, Use Cases & Tutorials===
The following screenshots illustrate how to use the filter and the expected results (note that the optimal parameters strongly depends on the characteristics of the image: voxel size, number of gradients...).

Before filtering:

{|
|[[Image:Orig.png|thumb|600px|Original unfiltered image]]
|}

After filtering:

{|
|[[Image:jLMMSE.png|thumb|600px|Original unfiltered image]]
|}

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood. A large radius more effectively reduces the noise but may induce a certain blurring of the edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. If N=0 is fixed, then all gradient directions are filtered together.
** NOTE: If N=1 is used this filter is similar (but not equal) to RicianLMMSEImageFilter. Two main differences exist: 1) 4-th order moments have to be computed only for baseline(s) image(s), and 2) if more than one baseline is present all of them are filtered together even if N=1.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===

Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/jointLMMSE link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:JointRicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:25:32Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.

The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

== Usage ==

The filter operates on an input DWI volume (gradient directions must be known). The meaning of the parameters of this module is listed below.

===Examples, Use Cases & Tutorials===
The following screenshots illustrate how to use the filter and the expected results (note that the optimal parameters strongly depends on the characteristics of the image: voxel size, number of gradients...).

Before filtering:

{|
|[[Image:Orig.png|thumb|600px|Original unfiltered image]]
|}

After filtering:

[[Image:jLMMSE.png|thumb|1000px|Seeding tracks from fiducial list]]

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood. A large radius more effectively reduces the noise but may induce a certain blurring of the edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. If N=0 is fixed, then all gradient directions are filtered together.
** NOTE: If N=1 is used this filter is similar (but not equal) to RicianLMMSEImageFilter. Two main differences exist: 1) 4-th order moments have to be computed only for baseline(s) image(s), and 2) if more than one baseline is present all of them are filtered together even if N=1.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===

Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/jointLMMSE link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:JointRicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:23:53Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.

The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

== Usage ==

The filter operates on an input DWI volume (gradient directions must be known). The meaning of the parameters of this module is listed below.

===Examples, Use Cases & Tutorials===
The following screenshots illustrate how to use the filter and the expected results (note that the optimal parameters strongly depends on the characteristics of the image: voxel size, number of gradients...).

Before filtering:

[[Image:Orig.png|thumb|1000px|Seeding tracks from fiducial list]]

After filtering:

[[Image:jLMMSE.png|thumb|1000px|Seeding tracks from fiducial list]]

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood. A large radius more effectively reduces the noise but may induce a certain blurring of the edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. If N=0 is fixed, then all gradient directions are filtered together.
** NOTE: If N=1 is used this filter is similar (but not equal) to RicianLMMSEImageFilter. Two main differences exist: 1) 4-th order moments have to be computed only for baseline(s) image(s), and 2) if more than one baseline is present all of them are filtered together even if N=1.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===

Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/jointLMMSE link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:JointRicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:22:32Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.

The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

== Usage ==

The filter operates on an input DWI volume (gradient directions must be known). The meaning of the parameters of this module is listed below.

===Examples, Use Cases & Tutorials===
The following screenshots illustrate how to use the filter and the expected results (note that the optimal parameters strongly depends on the characteristics of the image: voxel size, number of gradients...).

Before filtering:

[[Image:Orig.png|thumb|600px|Seeding tracks from fiducial list]]

After filtering:

[[Image:jLMMSE.png|thumb|600px|Seeding tracks from fiducial list]]

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood. A large radius more effectively reduces the noise but may induce a certain blurring of the edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. If N=0 is fixed, then all gradient directions are filtered together.
** NOTE: If N=1 is used this filter is similar (but not equal) to RicianLMMSEImageFilter. Two main differences exist: 1) 4-th order moments have to be computed only for baseline(s) image(s), and 2) if more than one baseline is present all of them are filtered together even if N=1.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===

Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/jointLMMSE link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:JointRicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:21:42Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.

The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

== Usage ==

The filter operates on an input DWI volume (gradient directions must be known). The meaning of the parameters of this module is listed below.

===Examples, Use Cases & Tutorials===
The following screenshots illustrate how to use the filter and the expected results (note that the optimal parameters strongly depends on the characteristics of the image: voxel size, number of gradients...).

Before filtering:
|[[Image:Orig.png|thumb|600px|Seeding tracks from fiducial list]]

After filtering:

[[File:jLMMSE.png]]

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood. A large radius more effectively reduces the noise but may induce a certain blurring of the edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. If N=0 is fixed, then all gradient directions are filtered together.
** NOTE: If N=1 is used this filter is similar (but not equal) to RicianLMMSEImageFilter. Two main differences exist: 1) 4-th order moments have to be computed only for baseline(s) image(s), and 2) if more than one baseline is present all of them are filtered together even if N=1.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===

Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/jointLMMSE link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Modules:JointRicianLMMSEImageFilter-Documentation-3.6

2010-05-17T08:20:23Z

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author: Antonio Tristán Vega and Santiago Aja Fernández
* Contact: atriveg@bwh.harvard.edu

===Module Description===
This module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.

The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.

A complete description of the algorithm may be found in:

Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.

== Usage ==

The filter operates on an input DWI volume (gradient directions must be known). The meaning of the parameters of this module is listed below.

===Examples, Use Cases & Tutorials===
The following screenshots illustrate how to use the filter and the expected results (note that the optimal parameters strongly depends on the characteristics of the image: voxel size, number of gradients...).

Before filtering:
|[[Image:Orig.png|thumb|280px|Seeding tracks from fiducial list]]
[[File:Orig.png]]

After filtering:

[[File:jLMMSE.png]]

===Quick Tour of Features and Use===
It is very easy to use it. Just select a DWI, set the parameters (if you really need it), and you're ready to go.

* '''Input DWI Volume:''' set the DWI volume
* '''Output DWI Volume:''' the filtered DWI volume
* '''Estimation radius:''' This is the 3D radius of the neighborhood used for noise estimation. Noise power is estimated as the mode of the histogram of local variances
* '''Filtering radius:''' This is the 3D radius of the neighborhood used for filtering: local means and covariance matrices are estimated within this neighborhood. A large radius more effectively reduces the noise but may induce a certain blurring of the edges.
* '''Number of neighborhood gradients:''' This filter works gathering joint information from the N closest gradient directions to the one under study. This parameter is N. If N=0 is fixed, then all gradient directions are filtered together.
** NOTE: If N=1 is used this filter is similar (but not equal) to RicianLMMSEImageFilter. Two main differences exist: 1) 4-th order moments have to be computed only for baseline(s) image(s), and 2) if more than one baseline is present all of them are filtered together even if N=1.

== Development ==

===Dependencies===

Volumes. Needed to load DWI volumes

===Known bugs===

===Usability issues===

===Source code & documentation===

Source Code: Follow this [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/DiffusionApplications/jointLMMSE link]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ComputeRestrictedHistogram.html itkComputeRestrictedHistogram.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1LMMSEVectorImageFilter.html itkLMMSEVectorImageFilter.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuStatistics.html itkOtsuStatistics.h]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1OtsuThreshold.html itkOtsuThreshold.h]

== More Information ==

===Acknowledgment===
Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid (SPAIN). Partially funded by grant number TEC2007-67073/TCM from the Ministerio de Ciencia e Innovación (Spain) and "FEDER" European Regional Development Fund.

===References===

* Antonio Tristán-Vega and Santiago Aja-Fernández, "DWI filtering using joint information for DTI and HARDI", Medical Image Analysis, Volume 14, Issue 2, Pages 205-218 (2010).
* Santiago Aja-Fernández, Antonio Tristán-Vega, and Carlos Alberola-López, "Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models". Magnetic Resonance Imaging, Volume 27, Pages 1397-1409 (2009).

Documentation/3.6

2010-05-17T08:19:11Z

Westin: /* Diffusion MRI */

=Documentation Draft notes=
Key for flagged modules below:

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

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

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

=Introduction=

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

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

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

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

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

=Main GUI=

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

=Modules=

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

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

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

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

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

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

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

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

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

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

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

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

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

==Slicer Extensions==

[[Documentation-3.6:ExtensionStatus|Extension Status]]

'''Introduction'''

* Slicer Extensions are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

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

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

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

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

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

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

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

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

'''Info for Developers'''

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

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

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

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

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

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

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

=Other information=

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

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

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

'''QA Table'''

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

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

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

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

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

Modules:DiffusionTensorScalarMeasurements-Documentation-3.6

2010-04-08T19:10:12Z

Westin:

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

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

{|
|[[Image:DiffusionTensorScalarMeasurementsGUI.png|thumb|280px|Caption 1]]
|}

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

Type: CLI

Category: Diffusion Tensor

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contact: [http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
This module computes scalar measurement from Diffusion Tensor Image (DTI) Volumes. Those scalar measurements are meant to represent properties of the Tensor like anisotropy or apparent diffusion.

== Usage ==

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

* Extract quantitative measurements of diffusivity from DTI volumes.

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

[http://www.na-mic.org/ViewVC/index.cgi/ Source code]

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

== More Information ==

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

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

Modules:DiffusionTensorEstimation-Documentation-3.6

2010-04-08T19:09:57Z

Westin:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
__NOTOC__
===Module Name===
Diffusion Tensor Estimation
{|
|[[Image:DiffusionTensorEstimationGUI.png|thumb|280px|Caption 1]]
|}
== General Information ==
===Module Type & Category===

Type: CLI

Category: Base or (Filtering, Registration, ''etc.'')

===Authors, Collaborators & Contact===
* Author: Raúl San José Estépar, BWH
* Contributor: Gordon Kindlmann, University of Chicago
* [http://lmi.bwh.harvard.edu/~rjosest/address.html Contact Information]

===Module Description===
This module estimates the diffusion tensor model from a Diffusion Weighted Image (DWI) Volume. The results is a tensor volume that can be used to compute different anisotropy measurements, for example Fractional Anisotropy, and perform tractography.

== Usage ==

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

* Compute DTI volume from DWI. It is the first step of any pipeline that employs DTI to assess white matter structure.

===Quick Tour of Features and Use===
The module takes one DWI volume and computes a DTI volume. The parameters are the following:
* '''Input/Output:''' Defines input and output files.
** ''Input DWI Volume'' is the input DWI volume,
** ''Output DTI Volume'' is the DTI volume that will be estimated.
** ''Output Baseline Volume'' is the average of the B0 images (non-diffusion weighted images) of the DWI sequence. This volume is useful to have a structural representation of the DTI volume .
** ''Otsu Threshold Mask'' is a approximated mask of the white matter that can be used to filter out the background.
* '''Estimation Parameters:'''
** ''Least Squares'': Least Squares estimation method. This is the method by default and stable [Basser, 2002].
** ''Weighted Least Squares'': WLS estimation method based on Salvador. This method implementation is still experimental [Salvador, 2005].
** ''Non-linear'': direct non-least squares fitting of the tensor model to the data without log-transformation. This method is experimental.
** ''Otsu Omega Threshold Parameter'': weight that controls the otsu threshold.
** ''Remove Island in Tensor Mask'': if active, holes in the produced mask will be removed.
** ''Apply Mask to Tensor Image'': Mask output DTI volume with the computed mask. Tensor outside the mask will be set to zero.

== Development ==

===Dependencies===

None

===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===

[http://www.na-mic.org/ViewVC/index.cgi/ Source code].

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

== More Information ==

===Acknowledgement===

===References===
*P. J. Basser and D. K. Jones. Diffusion-tensor MRI: theory, experimental design and data analysis - a technical review. NMR Biomed, 15(7-8):456–67, 2002.
*R. Salvador, A. Pena, D. K. Menon, T. A. Carpenter, J. D. Pickard, and E. T. Bullmore. Formal characterization and extension of the linearized diffusion tensor model. Hum Brain Mapp, 24(2):144–55, 2005.

Modules:UnbiasedNonLocalMeans-Documentation-3.6

2010-04-08T19:09:42Z

Westin:

Modules:RicianLMMSEImageFilter-Documentation-3.6

2010-04-08T19:09:26Z

Westin:

Westin: /* Diffusion MRI */

This is work in progress

=Main GUI=

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

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

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

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

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

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']]
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''

==Specialized Modules==

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

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) '''3.6 In Progress'''

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

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

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

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

===Diffusion MRI===
*Diffusion MRI
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
***[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''

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

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

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

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

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

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

=Slicer Extensions=

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

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

====Example Extensions====

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

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

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

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

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

'''Deprecated Extensions'''

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

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

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

Documentation/3.6

2010-04-07T14:51:07Z

Westin: /* Diffusion MRI */

This is work in progress

=Main GUI=

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

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

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

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

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

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

==Specialized Modules==

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

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) '''3.6 In Progress'''

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

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

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

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

===Diffusion MRI (C-F)===
*Diffusion MRI
** DWI data management
***[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
***[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''
***[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
***[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''

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

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

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

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

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

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

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

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

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

=Slicer Extensions=

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

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

====Example Extensions====

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

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

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

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

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

'''Deprecated Extensions'''

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

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

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