Slicer Wiki - User contributions [en]

Slicer 3.6:Training

2010-06-22T17:54:27Z

RandyGollub:

=Slicer 3.6 Tutorials=

* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.6 release) to accomplish certain tasks.
* For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
*For questions related to the Slicer3 Compendium, please send an e-mail to [http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]

{| border="1" cellpadding="5" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|'''Category'''
|'''Tutorial'''
|'''Sample Data'''
|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:Slicer3.6MinuteTutorial_SoniaPujol.pdf‎ | Slicer3Minute Tutorial]]''' The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.6. '''Audience:''' First time users.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/images/5/51/Slicer3MinuteDataset.zip Slicer3Minute Data]''' The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:3DDataLoadingAndVisualization_Slicer3.6_SoniaPujol.pdf‎ | Slicer3Visualization Tutorial]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginning users including clinicians, scientists, engineers and programmers.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Slicer3Visualization Data]''' The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.
| style="background:#FFFFCC; color:black" align="center"| [[Image:VisualizationTutorial 3.6RC3.png|200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| ''' [[media:ProgrammingIntoSlicer3_SoniaPujol.pdf |Programming in Slicer3 Tutorial]]''' The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin''']] The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.
| style="background:#FFFFCC; color:black" align="center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_SoniaPujol.pdf |Editor]] ''' Shows how to use the interactive editing tools in Slicer. '''Audience:''' All users and developers.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/index.php/File:EditorTutorialDataset.zip Editor Data]''' This dataset contains a MR dataset of the brain.
| style="background:#FFFFCC; color:black" align="center"| [[Image:InteractiveEditor.png|200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:Slicer3.6_Tutorial_ManualRegistration.pdf‎ | Manual Registration]] ''' Shows how to manually/interactively align two images in Slicer3.6 '''Audience:''' First time & early users.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/image/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]''' This dataset contains two brain MRI of a single subject, obtained in different orientations.
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3_ManualRegistrationTutorial.gif|200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:DiffusionMRITutorial_Slicer3.6_SPujol.pdf‎ | Diffusion MRI Tutorial ]]''' This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. '''Audience:''' All users and developers.
| style="background:#FFFFCC; color:black" valign="top" |''' [http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]'''
| style="background:#FFFFCC; color:black" align="center"| [[Image:cc.PNG |200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:Slicer3.6-ChangeTrackerTutorial.pdf‎ | Change Tracker Tutorial]]''' This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans. '''Audience:''' All users interested in longitudinal analysis of pathology.
| style="background:#FFFFCC; color:black" valign="top" |''' Training Data download is integrated with the ChangeTracker module (see Tutorial)'''
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3.4.1-ChangeTracker.jpg|200px]]
|}

=Software Installation=
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.

=Software Documentation=
*For the Slicer 3.6 manual pages please click [[Documentation-3.6|here]]. These pages are the reference manual for Slicer 3.6 and briefly explain the functionality found in panels and modules.

Slicer 3.6:Training

2010-06-22T17:53:49Z

RandyGollub:

=Slicer 3.6 Tutorials=

* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.6 release) to accomplish certain tasks.
* For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
*For questions related to the Slicer3 Compendium, please send an e-mail to [http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]

{| border="1" cellpadding="5" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|'''Category'''
|'''Tutorial'''
|'''Sample Data'''
|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:Slicer3.6MinuteTutorial_SoniaPujol.pdf‎ | Slicer3Minute Tutorial]]''' The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.6. '''Audience:''' First time users.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/images/5/51/Slicer3MinuteDataset.zip Slicer3Minute Data]''' The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3Minute_3.6RC2.png |200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:3DDataLoadingAndVisualization_Slicer3.6_SoniaPujol.pdf‎ | Slicer3Visualization Tutorial]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginning users including clinicians, scientists, engineers and programmers.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Slicer3Visualization Data]''' The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.
| style="background:#FFFFCC; color:black" align="center"| [[Image:VisualizationTutorial 3.6RC3.png|200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| ''' [[media:ProgrammingIntoSlicer3_SoniaPujol.pdf |Programming in Slicer3 Tutorial]]''' The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin''']] The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.
| style="background:#FFFFCC; color:black" align="center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_SoniaPujol.pdf |Editor]] ''' Shows how to use the interactive editing tools in Slicer. '''Audience:''' All users and developers.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/index.php/File:EditorTutorialDataset.zip Editor Data]''' This dataset contains a MR dataset of the brain.
| style="background:#FFFFCC; color:black" align="center"| [[Image:InteractiveEditor.png|200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:Slicer3.6_Tutorial_ManualRegistration.pdf‎ | Manual Registration]] ''' Shows how to manually/interactively align two images in Slicer3.6 '''Audience:''' First time & early users.
| style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/image/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]''' This dataset contains two brain MRI of a single subject, obtained in different orientations.
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3_ManualRegistrationTutorial.gif|200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:DiffusionMRITutorial_Slicer3.6_SPujol.pdf‎ | Diffusion MRI Tutorial ]]''' This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. '''Audience:''' All users and developers.
| style="background:#FFFFCC; color:black" valign="top" |''' [http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]'''
| style="background:#FFFFCC; color:black" align="center"| [[Image:cc.PNG |200px]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[media:Slicer3.6-ChangeTrackerTutorial.pdf‎ | Change Tracker Tutorial]]''' This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans. '''Audience:''' All users interested in longitudinal analysis of pathology.
| style="background:#FFFFCC; color:black" valign="top" |''' Training Data download is integrated with the ChangeTracker module (see Tutorial)'''
| style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3.4.1-ChangeTracker.jpg|200px]]
|}

=Software Installation=
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.

=Software Documentation=
*For the Slicer 3.6 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.6 and briefly explain the functionality found in panels and modules.

Slicer 3.6:Training

2010-06-22T17:52:03Z

RandyGollub:

Slicer3.4:Training

2010-06-22T17:45:07Z

RandyGollub:

=Slicer 3.4 Tutorials=

* Use this link to access the tutorials for the [[Slicer_3.6:Training |newest Slicer release (Slicer3.6)]].
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.4 release) to accomplish certain tasks.
* For questions related to the Slicer3.4 Compendium, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).

{| border="1" cellpadding="5" width="1000px"
|- style="background:#FFD700; color:#4A2A0A; font-size:130%" align="center"
| '''Category'''
| '''Tutorial'''
| '''Sample Data'''
| '''Image'''
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Basic'''
| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3Minute_SPujol.pdf | '''Slicer3Minute Tutorial''']] The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4. '''Audience:''' First time users.
| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute Data''']] The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3Minute.PNG|250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Basic'''
| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3_Tutorial_ManualRegistration.pdf| '''Slicer3 Manual Registration Tutorial''']] shows how to manually/interactively align two images in Slicer3.4 or 3.5 '''Audience:''' First time & early users.
| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip | '''Manual Registration Data''']] This dataset contains two brain MRI of a single subject, obtained in different orientations.
| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3_ManualRegistrationTutorial.gif|250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Core'''
| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf‎‎ | '''Slicer3Visualization Tutorial ''']] The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4. '''Audience:''' All beginning users including clinicians, scientists, engineers and programmers.
| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization Data''']] The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.
| style="background:#FDFC6D; color:black" align="center"| [[Image:DataLoadingAndVisualization_SPujol.png|250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Core'''
| style="background:#FDFC6D; color:black" valign="top" | [[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | '''Programming in Slicer3 Tutorial''']] The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FDFC6D; color:black" valign="top" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin''']] The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.
| style="background:#FDFC6D; color:black" align="center"| [[Image:ProgrammingCourse_Logo.PNG|250px|Programming]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FDFC6D; color:black" valign="top" | [[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | '''3D Visualization of FreeSurfer Data''']] The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4. '''Audience:''' All users.
| style="background:#FDFC6D; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip '''FreeSurfer Tutorial Data'''] The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
| style="background:#FDFC6D; color:black" align="center"| [[Image:FreeSurferTutorial.PNG|250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FDFC6D; color:black" valign="top" | [[Media:AutomaticSegmentation_SoniaPujol.pdf | '''Automatic Segmentation Tutorial''']] The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data. '''Audience:''' Programmers and Engineers.
| style="background:#FDFC6D; color:black" valign="top" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation Data''']]
| style="background:#FDFC6D; color:black" align="center"| [[Image:EMSegmentationTutorial.PNG|250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FDFC6D; color:black" valign="top" | [[Media:Slicer3_Tutorial_AtlasMerging_RegLib_C11-mj.ppt‎ | '''Atlas Label Merging & Surface Based Registration Tutorial ''']] This tutorial guides through the creation and co-registration of surface models of atlas structures (thalamus & thalamic nuclei) and subsequent merging of two labelmaps.
| style="background:#FDFC6D; color:black" valign="top" | [[Media:Slicer3_Tutorial_AtlasMerging_DataSet.zip| '''Atlas Merging Data''' (contains 2 full brain atlases + intermediate result files, 72MB)]]
| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3_SurfaceRegistrationTutorial_RegLib_C11.gif|250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FDFC6D; color:black" valign="top"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''Neurosurgical Planning Tutorial'''] This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules. '''Audience:''' All users interested in image-guided therapy.
| style="background:#FDFC6D; color:black" valign="top" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning Data ''']]
| style="background:#FDFC6D; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FDFC6D; color:black" valign="top" | [[Media:DiffusionMRITutorial_SFN2009_SPujol.pdf| '''Diffusion MRI Tutorial''']] This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. '''Audience:''' All users and developers.
| style="background:#FDFC6D; color:black" valign="top" | [[Media:DiffusionDataset.zip | '''Diffusion Data''']]
| style="background:#FDFC6D; color:black" align="center"| [[Image:cc.PNG |250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FDFC6D; color:black" valign="top" | [[Media:Slicer3.4.1-ChangeTrackerTutorial.pdf | '''ChangeTracker Tutorial''']] This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans.
'''Audience:''' All users interested in longitudinal analysis of pathology.
| style="background:#FDFC6D; color:black" valign="top" | [[Media:Slicer3.4.1-ChangeTrackerTutorial.pdf | '''Training Data download is integrated with the ChangeTracker module (see Tutorial)''']]
| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3.4.1-ChangeTracker.jpg |250px]]
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FDFC6D; color:black" valign="top" | [[Media:3DVisualizationLiverSegments_SoniaPujol_RSNA2009.pdf‎ | '''LiverSegmentation Tutorial''']] This tutorial introduces translational clinical scientists to the capabilities of the 3D Slicer software through the segmentation of the liver.
'''Audience:''' All users and developers.
| style="background:#FDFC6D; color:black" valign="top" | [[Media:LiverData_RSNA2009.tar.gz | '''Liver Segmentation Data''']]
| style="background:#FDFC6D; color:black" align="center"| [[Image:LiverSegmentation.png |250px]]
|}

= Slicer Tutorial Contest =

The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/AHM2010:Tutorial_Contest January 2010 Slicer tutorial contest], [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 June 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 January 2009 Slicer tutorial contest].

== '''January 2010 Slicer Tutorial Contest'''==

{| border="1" cellpadding="5" width="1000px"
|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"
|'''DBPs/Collaboration'''
|'''Tutorial'''
|'''Sample Data'''
|'''Image'''
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Fiber Clustering'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:FiberClusteringTrainingTutorial_Winter2010AHM.pdf‎| '''EM Fiber Clustering''']
| style="background:#CCFF99; color:black" valign="top" | [http://www.nitrc.org/projects/quantitativedti/‎ ‎ EM Fiber Clustering Data ]
| style="background:#CCFF99; color:black" align="center"| [[Image:Shot2.png |250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''VMTK'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariescenterlinesMRI_Winter2010AHM.pdf '''VMTK Coronary Arteries centerlines Extraction''']
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/images/a/aa/TutorialVMTKCoronariescenterlinesMRI_Data_Winter2010AHM.zip VMTK Centrelines Data]
| style="background:#CCFF99; color:black" align="center"| [[Image:Vmtkcloseupvoronoicenterlinewithreference.png|250px]]
|}

== '''June 2009 Slicer Tutorial Contest'''==

{| border="1" cellpadding="5" width="1000px"
|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"
|'''DBPs/Collaboration'''
|'''Tutorial'''
|'''Sample Data'''
|'''Image'''
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Confocal Microscopy'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf '''Confocal Microscopy''']
| style="background:#CCFF99; color:black" valign="top" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Data]
| style="background:#CCFF99; color:black" align="center"| [[Image:MicroscopyTutorial.png| 250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Autism'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf '''ARCTIC: Automatic Regional Cortical ThICkness''']
| style="background:#CCFF99; color:black" valign="top" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]
| style="background:#CCFF99; color:black" align="center"| [[Image:Corticalthickness.png| 250px ]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Prostate'''
| style="background:#CCFF99; color:black" valign="top"| [http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf ‎'''Trans-rectal MR guided prostate biopsy''']
| style="background:#CCFF99; color:black" valign="top" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR-guided Prostate Biopsy Data]]
| style="background:#CCFF99; color:black" align="center"| [[Image:TransRectalBiopsy.png| 250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Schizophrenia'''
| style="background:#CCFF99; color:black" valign="top" | [[media:Stochastic_June09_3.ppt| '''Python Stochastic Tractography Module''']]
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]
| style="background:#CCFF99; color:black" align="center"| [[Image:StochasticTractographyTutorial2.png|250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Lupus'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf '''White Matter Lesions Segmentation''']
| style="background:#CCFF99; color:black" valign="top"| [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]
| style="background:#CCFF99; color:black" align="center"| [[Image:LupusTutorial2.PNG| 250px]]
|-
|}

== '''January 2009 Slicer Tutorial Contest'''==

{| border="1" cellpadding="5" width="1000px"
|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"
|'''DBPs/Collaboration'''
|'''Tutorial'''
|'''Sample Data'''
|'''Image'''
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Automated FE Mesh'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf '''IA FEMesh Tutorial''']
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]
| style="background:#CCFF99; color:black" align="center"| [[Image:Femesh-in-trunk-120808.png|250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Alcohol and Stress Interaction'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf '''Non-Human Primate Segmentation Tutorial''']
| style="background:#CCFF99; color:black" valign="top" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]
| style="background:#CCFF99; color:black" align="center"| ‎[[Image: Non-HumanPrimateSegmentation.png|250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Prostate'''
| style="background:#CCFF99; color:black" valign="top"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning '''MR-guided Prostate Interventions''']
| style="background:#CCFF99; color:black" valign="top"| [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]
| style="background:#CCFF99; color:black" align="center"|[[Image:ProstatePlanningOverview.png | 250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''IGT'''
| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial '''Basic Navigation Tutorial''']
| style="background:#CCFF99; color:black" valign="top"| [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]
| style="background:#CCFF99; color:black" align="center"| [[Image:300px-IGTBasicNavigationSummary.png| 250px]]
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| '''Orbit Segmentation'''
| style="background:#CCFF99; color:black" valign="top"| [[Media:OrbitSegmentationTutorial.pdf‎| '''Segmentation of the Orbit''']]
| style="background:#CCFF99; color:black" valign="top"| [[Media:OrbiteSegmentationData.zip‎ ‎| Orbit Segmentation Data ]]
| style="background:#CCFF99; color:black" align="center"| [[Image:OrbitSegmentationt.png |250px]]
|-
|}

= Slicer 3.5 Tutorials=

*The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.5) to accomplish certain tasks.

{| border="1" cellpadding="5" width="1000px"
|- style="background:#547389; color:#994139; font-size:130%" align="center"
|'''Contest'''
|'''Tutorial'''
|'''Sample Data'''
|'''Image'''
|-
| style="background:#547389; color:#994139; font-size:110%" align="center"| '''Specialized'''
| style="background:#b7cfd7; color:black" valign="top"| [http://www.na-mic.org/Wiki/index.php/RobustStatisticsSegmentation‎ '''Robust Statistics Segmentation Tutorial''']
| style="background:#b7cfd7; color:black" valign="top" | [[Media:Patient1.tar.gz | '''Robust Statistics Segmentation Data''']]
| style="background:#b7cfd7; color:black" align="center"| [[Image:RobustStatisticsSegmentation LiverSpleenKidney.png |250px]]
|-
|}

=Software Installation=
*The [http://www.slicer.org/pages/Special:SlicerDownloads '''Slicer download page'''] contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.

=Software Documentation=
*For the Slicer 3.4 manual pages please click [[Documentation-3.4|here]]. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.

=Older Tutorials=
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].