Slicer Wiki - User contributions [en]

File:ScreenshotLobeSegmentation.png

2014-01-09T19:11:27Z

Raul: Semi-automatic lobe segmentation as part of the Chest Imaging Platform

Semi-automatic lobe segmentation as part of the Chest Imaging Platform

Slicer4:VisualBlog

2014-01-09T19:10:04Z

Raul:

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

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

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

Slicer4:VisualBlog

2014-01-09T19:07:25Z

Raul:

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

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

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

Slicer4:VisualBlog

2014-01-09T19:06:23Z

Raul:

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

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

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

Documentation/3.6

2010-05-20T02:02:51Z

Raul: /* Diffusion MRI */

=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)
*[[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
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex 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
**[[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)
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| 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)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| 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
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit)
*** [[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-3.6|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)

=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

Modules:ROISeeding-Documentation-3.6

2010-05-20T01:56:22Z

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

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: [http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
Labelmap Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module [http://wiki.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6]

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input / Output:'''
** Input DTI Volume: set the input DTI volume that is going to be used for tractography.
** Input Label Map: set the labelmap volume that is going to be used for seeding.
** Output Fiber bundle: set the resulting fiber bundle that is going to store the result.
** Write Fibers to Disk: option to save the results to disk for further analysis.
** Output directory: path where the results are saved.
** File Prefix Name: name that would be used for each output bundle.
* '''Seed Placement Options'''
** Seed Spacing: spacing in between seed points within in the labelmap (in mm).
** Random grid: use random placement.
** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
* '''Tractography Seeding Parameters:'''
** Minimum Length:
** Maximum Length:
* '''Label Definition:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

[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:ROISeeding-Documentation-3.6

2010-05-20T01:55:59Z

Raul: /* Authors, Collaborators & Contact */

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: [http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
Labelmap Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module [http://wiki.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6]

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input / Output:'''
** Input DTI Volume: set the input DTI volume that is going to be used for tractography.
** Input Label Map: set the labelmap volume that is going to be used for seeding.
** Output Fiber bundle: set the resulting fiber bundle that is going to store the result.
** Write Fibers to Disk: option to save the results to disk for further analysis.
** Output directory: path where the results are saved.
** File Prefix Name: name that would be used for each output bundle.
* '''Seed Placement Options'''
** Seed Spacing: spacing in between seed points within in the labelmap (in mm).
** Random grid: use random placement.
** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
* '''Tractography Seeding Parameters:'''
** Minimum Length:
** Maximum Length:
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

[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:ROISeeding-Documentation-3.6

2010-05-19T22:45:02Z

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

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
Labelmap Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module [http://wiki.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6]

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input / Output:'''
** Input DTI Volume: set the input DTI volume that is going to be used for tractography.
** Input Label Map: set the labelmap volume that is going to be used for seeding.
** Output Fiber bundle: set the resulting fiber bundle that is going to store the result.
** Write Fibers to Disk: option to save the results to disk for further analysis.
** Output directory: path where the results are saved.
** File Prefix Name: name that would be used for each output bundle.
* '''Seed Placement Options'''
** Seed Spacing: spacing in between seed points within in the labelmap (in mm).
** Random grid: use random placement.
** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
* '''Tractography Seeding Parameters:'''
** Minimum Length:
** Maximum Length:
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

[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:ROISeeding-Documentation-3.6

2010-05-19T20:17:28Z

Raul: /* Module Description */

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
Labelmap Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module [http://wiki.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6]

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

[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.

File:LabelmapSeeding.png

2010-05-19T20:09:44Z

Raul:

Modules:ROISeeding-Documentation-3.6

2010-05-19T20:09:26Z

Raul: /* Module Name */

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

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

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

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

[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:ROISeeding-Documentation-3.6

2010-05-19T19:44:09Z

Raul: /* Module Type & Category */

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

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

{|
|[[Image:roi_tract.jpg|thumb|280px|Caption 1]]
|}

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

Type: CLI

Category: Diffusion MRI Applications

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

[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

2010-05-19T19:43:48Z

Raul: /* Module Type & Category */

[[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: Diffusion MRI Applications

===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 result 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 an 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 the most stable [Basser, 2002].
** ''Weighted Least Squares'': WLS estimation method based on Salvador's method that takes into account the Rician noise model in the MRI signal to weight the least square fitting by the magnitude of the DWI signal. 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===
This module has been developed at Laboratory of Mathematics in Imaging (LMI). The functionality of this module is provided by the Teem library (http://teem.sourceforge.net/)
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

===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:DiffusionTensorEstimation-Documentation-3.6

2010-05-19T19:19:57Z

Raul: /* Acknowledgement */

[[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 result 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 an 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 the most stable [Basser, 2002].
** ''Weighted Least Squares'': WLS estimation method based on Salvador's method that takes into account the Rician noise model in the MRI signal to weight the least square fitting by the magnitude of the DWI signal. 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===
This module has been developed at Laboratory of Mathematics in Imaging (LMI). The functionality of this module is provided by the Teem library (http://teem.sourceforge.net/)
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

===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:DiffusionTensorScalarMeasurements-Documentation-3.6

2010-05-19T19:15:24Z

Raul: /* Acknowledgment */

[[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 measurements from Diffusion Tensor Image (DTI) Volumes. Those scalar measurements represent invariant 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===
The module takes one DTI volume and computes a scalar volume. The parameters are the following:
* '''Input/Output:'''
** ''Input DTI Volume'' is the input DTI volume,
** ''Output Scalar Volume'' is the scalar volume with the resulting measurement
* '''Operation panel:'''
** Quantities to compute from the DTI volume.

== 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===
This module has been developed at Laboratory of Mathematics in Imaging (LMI). This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

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

Modules:DiffusionTensorScalarMeasurements-Documentation-3.6

2010-05-19T19:05:45Z

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

[[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 measurements from Diffusion Tensor Image (DTI) Volumes. Those scalar measurements represent invariant 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===
The module takes one DTI volume and computes a scalar volume. The parameters are the following:
* '''Input/Output:'''
** ''Input DTI Volume'' is the input DTI volume,
** ''Output Scalar Volume'' is the scalar volume with the resulting measurement
* '''Operation panel:'''
** Quantities to compute from the DTI volume.

== 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:DiffusionTensorScalarMeasurements-Documentation-3.6

2010-05-19T19:04:00Z

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

[[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 measurements from Diffusion Tensor Image (DTI) Volumes. Those scalar measurements represent invariant 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===
The module takes one DTI volume and computes a scalar volume. The parameters are the following:
* '''Input/Output:'''
** ''Input DTI Volume'' is the input DTI volume,
** ''Output Volume'' is the scalar volume with the resulting measurement
* '''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:DiffusionTensorScalarMeasurements-Documentation-3.6

2010-05-19T19:01:41Z

Raul: /* Module Description */

[[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 measurements from Diffusion Tensor Image (DTI) Volumes. Those scalar measurements represent invariant 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

2010-05-19T18:47:49Z

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

[[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 result 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 an 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 the most stable [Basser, 2002].
** ''Weighted Least Squares'': WLS estimation method based on Salvador's method that takes into account the Rician noise model in the MRI signal to weight the least square fitting by the magnitude of the DWI signal. 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:DiffusionTensorEstimation-Documentation-3.6

2010-05-19T18:44:55Z

Raul: /* Module Description */

[[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 result 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.

File:DiffusionTensorScalarMeasurementsGUI.png

2009-04-14T20:52:08Z

Raul:

Modules:DiffusionTensorScalarMeasurements-Documentation-3.4

2009-04-14T20:51:57Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__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===

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

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

== More Information ==

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

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

File:DiffusionTensorEstimationGUI.png

2009-04-14T20:33:17Z

Raul:

Modules:DiffusionTensorEstimation-Documentation-3.4

2009-04-14T20:32:54Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__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===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Gordon Kindlmann, University of Chicago
* Contact: [http://lmi.bwh.harvard.edu/~rjosest/address.html]

===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===

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

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

== More Information ==

===Acknowledgment===

===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:DiffusionTensorEstimation-Documentation-3.4

2009-04-14T20:25:57Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

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

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

Type: CLI

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

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Gordon Kindlmann, University of Chicago
* Contact: [http://lmi.bwh.harvard.edu/~rjosest/address.html]

===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===

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

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

== More Information ==

===Acknowledgment===

===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:ROISeeding-Documentation-3.4

2009-03-17T19:22:15Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:roi_tract.jpg|thumb|280px|Caption 1]]
|}

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

Type: CLI

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

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

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

== More Information ==

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

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

Modules:ROISeeding-Documentation-3.4

2009-03-17T19:20:46Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:roi_tract.jpg|thumb|280px|Caption 1]]
|}

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

Type: CLI

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

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

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

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

== More Information ==

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

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

Modules:ROISeeding-Documentation-3.4

2009-03-17T19:19:04Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

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

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

Type: CLI

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

===Authors, Collaborators & Contact===
* Author1: Raúl San José Estépar, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

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

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

== More Information ==

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

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

Modules:DiffusionTensorEstimation-Documentation-3.4

2009-03-17T19:17:52Z

Raul:

Modules:DiffusionTensorEstimation-Documentation-3.4

2009-03-17T19:17:15Z

Raul:

Modules:DiffusionTensorEstimation-Documentation-3.4

2009-03-17T19:16:50Z

Raul:

Modules:DiffusionTensorEstimation-Documentation-3.4

2009-03-17T19:16:31Z

Raul:

Modules:ROISeeding-Documentation-3.4

2009-03-17T14:03:44Z

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

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

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

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

Type: CLI

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

===Authors, Collaborators & Contact===
* Author1: Raul San Jose, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: Raul San Jose, lmi.bwh.harvard.edu/~rjosest

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
**First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
**Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

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

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

== More Information ==

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

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

Modules:ROISeeding-Documentation-3.4

2009-03-17T13:52:16Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

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

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

Type: CLI

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

===Authors, Collaborators & Contact===
* Author1: Raul San Jose, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: Raul San Jose, lmi.bwh.harvard.edu/~rjosest

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study. First, a region of interest in the tract that is under study has to be defined, for example by manually delineating the ROI using the Editor module. Second, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation]. Thrid, start the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].

== 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===

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

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

== More Information ==

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

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

Modules:ROISeeding-Documentation-3.4

2009-03-17T13:50:07Z

Raul:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

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

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

Type: CLI

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

===Authors, Collaborators & Contact===
* Author1: Raul San Jose, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: Raul San Jose, lmi.bwh.harvard.edu/~rjosest

===Module Description===
ROI Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study. First, a region of interest in the tract that is under study has to be defined, for example by manually delineating the ROI using the Editor module. Second, the DWI has to be loaded and the tensor has to be created using the [Diffusion Tensor Estimation | Modules:DiffusionTensorEstimation-Documentation-3.4]. Thrid, start the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [Filtering -> Resample Volume 2 | http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4].

== 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===

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

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

== More Information ==

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

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

Modules:ROISeeding-Documentation-3.4

2009-02-24T06:53:38Z

Raul: New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Module Name=== MyModule {| |Caption 1 |[[Image:screenshotBlank.png|thumb|28...

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

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

Type: Interactive or CLI

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

===Authors, Collaborators & Contact===
* Author1: Affiliation & logo, if desired
* Contributor1: Affiliation & logo, if desired
* Contributor2: Affiliation & logo, if desired
* Contact: name, email

===Module Description===
Overview of what the module does goes here.

== Usage ==

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

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

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

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

== Development ==

===Dependencies===

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

===Known bugs===

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

===Usability issues===

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

===Source code & documentation===

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

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

== More Information ==

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

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

Modules:DiffusionTensorScalarMeasurements-Documentation-3.4

2009-02-24T06:53:08Z

Raul: New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Module Name=== MyModule {| |Caption 1 |[[Image:screenshotBlank.png|thumb|28...

Modules:DiffusionTensorEstimation-Documentation-3.4

2009-02-24T06:52:38Z

Raul: New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Module Name=== MyModule {| |Caption 1 |[[Image:screenshotBlank.png|thumb|28...

Documentation/3.4

2009-02-24T06:50:27Z

Raul:

Note: This page is currently under construction

=Introduction=
[[Image:Base-Features-and-Modules.png|thumb|right|overview|[[Media:Integrating with Slicer3.ppt | Integrating with Slicer3]]]]
This page is a portal for documentation about Slicer 3.4.
For information for software developers, please go to the Developers page (see link in navigation box to the left).

=How-To Tutorials=
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]

=Feature Request and Problem Reports=
We have an issues [http://www.na-mic.org/Bug/my_view_page.php tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.

=List of Modules in need of documentation=
== Requirements for modules to be added to the release==
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''' for the tasks advertised on 2-4-2009
* 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-3.4#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.4#Modules|'''here''']] to structure your page.
*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 '''Acknowledgment''' tab of the module. Please see the '''Models module''' for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.
** '''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.)
* If your module has [[Documentation-3.2|documentation in Slicer 3.2]], please copy/paste/update into the 3.4 version
| 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]]
|}

==Main GUI==
*[[Modules:MainApplicationGUI-Documentation-3.4| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.4| List of Hotkeys and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.4| How to load data]] (Steve Pieper)
*[[Modules:Saving-Documentation-3.4| Save Scene and Data Module]] (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-3.4_Template|Slicer3:Module_Documentation-3.4_Template]]
*See above 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]]
===Core and Loadable Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)

*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)

==Other Modules==

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)
===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)
===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)

===Batch processing===
*[[Modules:EMSegment-Documentation-3.4|EM Segementer batch]] (Stephen Aylward)
*[[Modules:GaussianBlur-Documentation-3.4|Gaussian blur batch]] (Stephen Aylward)
*[[Modules:Registration-Documentation-3.4|Registration batch]] (Stephen Aylward)
===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)

===Demonstration===
*[[Modules:ExecutionModelTour-Documentation-3.4|Execution Model Tour]] (Daniel Blezek, Bill Lorensen)
*Scripted Module Example (Steve Pieper)

===Filtering===
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)
*Extract Skeleton (Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)
*Threshold Image (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**Gaussian Blur (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen)

*Freesurfer Surface Section Extraction (Katharina Quintus)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)
*Distance Transform Model (Steve Pieper)
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)
*Probe Volume with Model (Paint) (Lauren O'Donnell)

===Python Modules===
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonScript-Documentation-3.4| Python Script]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonNumpyScript-Documentation-3.4| Python Numpy Script]] (Luca Antiga, Daniel Blezek)

===Registration===
*Affine Registration (Daniel Blezek)
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)
*Diffeomorphic Demons Algorithm (Tom Vercauteren, Enger Konukoglu, Kilian Pohl)
*Linear Registration (Daniel Blezek)
*Realign Volume (Nicole Aucoin)
*Rigid Registration (Daniel Blezek)
*Test Grid Transform Registration (Yinglin Lee)
*(Utah) Deformable B-Spline Registration (Experimental) (Sam Gerber, Jim Miller, Steve Pieper, Ross Whitaker)

===Segmentation===
*EM Segment Command-Line (Brad Davis, Will Schroeder)
*EM Segment Simple (Brad Davis, Will Schroeder)
*EMSegmentTemplateBuilder (Brad Davis, Will Schroeder)
*Simple Region Growing (Jim Miller)
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)

===Statistics===
*Calculate Volume Statistics (Tri Ngo)
*Label Statistics (Steve Pieper)

===DWI and Tractography===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**Python Diffusion Tensor Estimation (Julien von Siebenthal)
*Python Extract Baseline DWI Volume (Julien von Siebenthal)
*Filter
**Joint Rician LMMSE Image Filter (Antonio Tritan Vega, Santiago Aja Fernandez)
**Rician LMMSE Image Filter (Antonio Tritan Vega, Santiago Aja Fernandez)
**Unbiased Non Local Means filter for DWI (Antonio Tritan Vega, Santiago Aja Fernandez)
*Python Shift DWI Values (Julien von Siebenthal)
*Python Recenter Scalar to DWI Volume (Julien von Siebenthal)
====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)
*[[Modules:DTIDisplay-Documentation-3.4|Display]] (Alex Yarmakovich)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
*Analysis
**[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
**ROI Select (Lauren O'Donnell)
**[[Modules:ROISeeding-Documentation-3.4 | ROI Seeding]] (Raul San Jose Estepar)
**Python Stochastic Tractography (Julien von Siebenthal)

=Documented Modules=
(please do not touch this section for now. Ron)
==Main GUI==

==Modules==

===Core and Loadable Modules===

==CLI Modules==

=Modules for Downloading=
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
We are using NITRC as a repository for contributed modules. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.

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 modules on NITRC.

Work is in progress to create infrastructure for searching an loading modules. See [[Slicer3:Loadable_Modules:Status_2009-01-20|here]] for more information.