Difference between revisions of "Slicer3.4:Training"

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= Slicer 3.4 Tutorials =
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=Slicer 3.4 Tutorials=
  
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.4) to accomplish certain tasks.  
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* For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
 +
* 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).
 
* 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"
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{| border="1" cellpadding="5" width="1000px"
|- style="background:#FFD700; color:#4A2A0A; font-size:130%" align="center"  
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|- style="background:#FFD700; color:#4A2A0A; font-size:130%" align="center"
| style="width:8%" ;align="Center"| '''Category'''
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| '''Category'''
| style="width:40%" ;align="Center"| '''Tutorial'''
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| '''Tutorial'''
| style="width:40%" ;align="Center"| '''Sample Data'''  
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| '''Sample Data'''
| style="width:12%" ;align="Center"| '''Image'''
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| '''Image'''
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"|<span id="1.1"></span> '''Basic'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"|<span id="1.1"></span> '''Basic'''
| style="background:#FDFC6D; color:black" | '''[[Media:Slicer3Minute_SPujol.pdf | Slicer3Minute Tutorial]]''' <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience''': First time users.   
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| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3Minute_SPujol.pdf | '''Slicer3Minute Tutorial''']] <br><br> The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.<br> <br>'''Audience:''' First time users.   
| style="background:#FDFC6D; color:black"| [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute dataset''' ]]<br><br> The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
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| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3MinuteDataset.zip | '''Slicer3Minute Data''']]<br><br> 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3Minute.PNG|250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"|<span id="1.1"></span> '''Basic'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"|<span id="1.1"></span> '''Basic'''
| style="background:#FDFC6D; color:black" | '''[[Media:Slicer3_Tutorial_ManualRegistration.pdf| Slicer3 Manual Registration Tutorial]]''' <br><br> shows how to manually/interactively align two images in Slicer3.4 or 3.5<br> <br>'''Audience''': First time & early users.   
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| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3_Tutorial_ManualRegistration.pdf| '''Slicer3 Manual Registration Tutorial''']] <br><br> shows how to manually/interactively align two images in Slicer3.4 or 3.5<br> <br>'''Audience:''' First time & early users.   
| style="background:#FDFC6D; color:black"| [[Media:Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip | '''Manual Registration example dataset''' ]]<br><br> This dataset contains two brain MRI  of a single subject, obtained in different orientations.
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| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip | '''Manual Registration Data''']]<br><br> 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3_ManualRegistrationTutorial.gif|250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"|<span id="1.2"></span> '''Core'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"|<span id="1.2"></span> '''Core'''
| style="background:#FDFC6D; color:black"|[[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf‎‎ | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br> '''Audience''': All beginning users including clinicians, scientists, engineers and programmers.
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| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3Course_DataLoading_3DVisualization_SoniaPujol.pdf‎‎ | '''Slicer3Visualization Tutorial ''']] <br><br> The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.<br> <br>'''Audience:''' All beginning users including clinicians, scientists, engineers and programmers.
| style="background:#FDFC6D; color:black" | [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization dataset''' ]] <br><br> The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.
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| style="background:#FDFC6D; color:black" valign="top"| [[Media:Slicer3VisualizationDataset.zip | '''Slicer3Visualization Data''']] <br><br> 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:DataLoadingAndVisualization_SPujol.png|250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Core'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Core'''
| style="background:#FDFC6D; color:black" | '''[[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | Programming in Slicer3 Tutorial ]]''' <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience''': Programmers and Engineers.   
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:ProgrammingIntoSlicer3_SoniaPujol.pdf | '''Programming in Slicer3 Tutorial''']] <br><br> The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br> <br>'''Audience:''' Programmers and Engineers.   
| style="background:#FDFC6D; color:black" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin ''']]<br><br> 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.
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin''']]<br><br> 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:ProgrammingCourse_Logo.PNG|250px|Programming]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FDFC6D; color:black" | '''[[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | 3D Visualization of FreeSurfer Data ]]''' <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience''': All users.   
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:FreeSurferCourse_Slicer3-4_SoniaPujol.pdf | '''3D Visualization of FreeSurfer Data''']] <br><br> The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.<br> <br>'''Audience:''' All users.   
| style="background:#FDFC6D; color:black" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip  '''FreeSurfer Tutorial dataset ''']<br><br> The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
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| style="background:#FDFC6D; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip  '''FreeSurfer Tutorial Data''']<br><br> 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:FreeSurferTutorial.PNG|250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FDFC6D; color:black" | '''[[Media:AutomaticSegmentation_SoniaPujol.pdf | Automatic Segmentation Tutorial ]]''' <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience''': Programmers and Engineers.   
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:AutomaticSegmentation_SoniaPujol.pdf | '''Automatic Segmentation Tutorial''']] <br><br> The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.<br> <br>'''Audience:''' Programmers and Engineers.   
| style="background:#FDFC6D; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]  
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation Data''']]  
| style="background:#FDFC6D; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|250px]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:EMSegmentationTutorial.PNG|250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FDFC6D; color:black" | '''[[Media:Slicer3_Tutorial_AtlasMerging_RegLib_C11-mj.ppt‎ |Atlas Label Merging & Surface Based Registration Tutorial ]]''' <br><br> This tutorial guides through the creation and co-registration of surface models of atlas structures (thalamus & thalamic nuclei) and subsequent merging of two labelmaps.
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:Slicer3_Tutorial_AtlasMerging_RegLib_C11-mj.ppt‎ | '''Atlas Label Merging & Surface Based Registration Tutorial ''']] <br><br> 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" | [[Media:Slicer3_Tutorial_AtlasMerging_DataSet.zip| '''Atlas Merging tutorial dataset''' (contains 2 full brain atlases + intermediate result files, 72MB)]]  
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| 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3_SurfaceRegistrationTutorial_RegLib_C11.gif|250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FDFC6D; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning Tutorial ]''' <br><br> 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.<br> <br>'''Audience''': All users interested in image-guided therapy.   
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| style="background:#FDFC6D; color:black"  valign="top"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''Neurosurgical Planning Tutorial'''] <br><br> 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.<br> <br>'''Audience:''' All users interested in image-guided therapy.   
| style="background:#FDFC6D; color:black" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning dataset ''']]  
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning Data ''']]  
| style="background:#FDFC6D; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FDFC6D; color:black" | [[Media:DiffusionMRITutorial_SFN2009_SPujol.pdf| '''Diffusion MRI Tutorial''']] <br><br> This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles.
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:DiffusionMRITutorial_SFN2009_SPujol.pdf| '''Diffusion MRI Tutorial''']] <br><br> This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles.<br> <br>'''Audience:''' All users and developers.  
'''Audience''': All users and developers.  
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:DiffusionDataset.zip | '''Diffusion Data''']]  
| style="background:#FDFC6D; color:black" | [[Media:DiffusionDataset.zip | '''Diffusion dataset ''']]  
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| style="background:#FDFC6D; color:black" align="center"| [[Image:cc.PNG |250px]]
| style="background:#FDFC6D; color:black" align="Center"| [[Image:cc.PNG |250px]]
 
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FDFC6D; color:black" | '''[[Media:Slicer3.4.1-ChangeTrackerTutorial.pdf | ChangeTracker Tutorial]]''' <br><br> This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans.
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:Slicer3.4.1-ChangeTrackerTutorial.pdf | '''ChangeTracker Tutorial''']] <br><br> 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.
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'''Audience:''' All users interested in longitudinal analysis of pathology.
| style="background:#FDFC6D; color:black" | '''[[Media:Slicer3.4.1-ChangeTrackerTutorial.pdf | Training data download is integrated with the ChangeTracker module (see Tutorial)''']]
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| 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3.4.1-ChangeTracker.jpg |250px]]
 
|-
 
|-
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FDFC6D; color:black" | '''[[Media:3DVisualizationLiverSegments_SoniaPujol_RSNA2009.pdf‎ | LiverSegmentation Tutorial]]''' <br><br> This tutorial introduces translational clinical scientists to the capabilities of the 3D Slicer software through the segmentation of the liver.
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| style="background:#FDFC6D; color:black" valign="top" | [[Media:3DVisualizationLiverSegments_SoniaPujol_RSNA2009.pdf‎ | '''LiverSegmentation Tutorial''']] <br><br> 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.
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'''Audience:''' All users and developers.
| style="background:#FDFC6D; color:black" | [[Media:LiverData_RSNA2009.tar.gz | '''Liver Segmentation dataset ''']]
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| 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]]
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| style="background:#FDFC6D; color:black" align="center"| [[Image:LiverSegmentation.png |250px]]
 
|}
 
|}
  
= Slicer Tutorial Contest '''(under construction)'''=
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= 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].
  
The following tutorials were part of the [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2009 Summer 2009 Slicer tutorial contest] and [http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJan2009 Winter 2009 Slicer tutorial contest].
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== '''January 2010 Slicer Tutorial Contest'''==
  
 
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{| border="1" cellpadding="5" width="1000px"
{| border="1" cellpadding="5"
 
 
|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"  
 
|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"  
| style="width:8%" ;align="Center"| '''Driving Biological Project/Collaboration'''
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|'''DBPs/Collaboration'''
| style="width:40%" ;align="Center"| '''Tutorial'''
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|'''Tutorial'''
| style="width:40%" ;align="Center"| '''Sample Data'''  
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|'''Sample Data'''
| style="width:12%" ;align="Center"| '''Image'''
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|'''Image'''
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Confocal Microscopy'''
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| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Fiber Clustering'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/4d/Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf Confocal Microscopy] '''  
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| style="background:#CCFF99; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/images/c/c7/FiberClusteringTrainingTutorial_Winter2010AHM.pdf '''EM Fiber Clustering''']
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm Microscopy Confocal Dataset]
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| 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:MicroscopyTutorial.png| 250px]]
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| style="background:#CCFF99; color:black" align="center"| [[Image:Shot2.png |250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Autism'''
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| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''VMTK'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] '''  
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| style="background:#CCFF99; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf '''VMTK Coronary Arteries centerlines Extraction''']
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]
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| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/index.php/File:TutorialVMTKCoronariesCenterlinesMRI_Data_Winter2010AHM.zip VMTK Centrelines Data]
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 250px ]]
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| 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"| <span id="1.1"></span> '''Prostate'''
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| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Confocal Microscopy'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf ‎Trans-rectal MR guided prostate biopsy] '''  
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| 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" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]
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| 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:TransRectalBiopsy.png| 250px]]
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| style="background:#CCFF99; color:black" align="center"| [[Image:MicroscopyTutorial.png| 250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Schizophrenia'''
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| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Autism'''
| style="background:#CCFF99; color:black" | [[media:Stochastic_June09_3.ppt| '''Python Stochastic Tractography Module''']]  
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| style="background:#CCFF99; color:black" valign="top" | [http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf '''ARCTIC: Automatic Regional Cortical ThICkness''']
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]
+
| style="background:#CCFF99; color:black" valign="top" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|250px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:Corticalthickness.png| 250px ]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Lupus'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Prostate'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.2.1.pdf White Matter Lesions Segmentation V2.2] '''  
+
| 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" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]
+
| style="background:#CCFF99; color:black" valign="top" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR-guided Prostate Biopsy Data]]
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 250px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:TransRectalBiopsy.png| 250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Automated FE Mesh'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Schizophrenia'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] '''  
+
| style="background:#CCFF99; color:black" valign="top" | [[media:Stochastic_June09_3.ppt| '''Python Stochastic Tractography Module''']]
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MeshTutorialExampleData.zip Mesh Tutorial Example Data]
+
| 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:Femesh-in-trunk-120808.png |250px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:StochasticTractographyTutorial2.png|250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Alcohol and Stress Interaction'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Lupus'''
| style="background:#CCFF99; color:black" | '''[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.na-mic.org/Wiki/images/7/7c/Slicer3Training_WhiteMatterLesions_v2.2.1.pdf '''White Matter Lesions Segmentation''']
| style="background:#CCFF99; color:black" | [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation Data]
+
| 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: Non-HumanPrimateSegmentation.png|250px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:LupusTutorial2.PNG| 250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Prostate'''
+
|}
| style="background:#CCFF99; color:black" | '''[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning MR Guided Prostate Interventions ]'''
+
 
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions Data]
+
== '''January 2009 Slicer Tutorial Contest'''==
| style="background:#CCFF99; color:black" align="Center"|[[Image:ProstatePlanningOverview.jpg | 250px]]
+
 
|-
+
{| border="1" cellpadding="5" width="1000px"
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''IGT'''
+
|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"  
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial] '''  
+
|'''DBPs/Collaboration'''
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation Data]
+
|'''Tutorial'''
| style="background:#CCFF99; color:black" align="Center"| [[Image:300px-IGTBasicNavigationSummary.png| 250px]]
+
|'''Sample Data'''
 +
|'''Image'''
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Schizophrenia'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Automated FE Mesh'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] '''  
+
| 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" | [http://www.na-mic.org/Wiki/index.php/File:IJdata.tar.gz Stochastic Tractography Data]
+
| 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:StochasticTractographyTutorial2.png| 250px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:Femesh-in-trunk-120808.png|250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Autism'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Alcohol and Stress Interaction'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V1.0]'''  
+
| 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" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]
+
| style="background:#CCFF99; color:black" valign="top" | [[media:SlicerTutorialData_Vervet.tar.gz‎ | Non-Human Primate Segmentation Data]]
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png‎|250px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image: Non-HumanPrimateSegmentation.png|250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Lupus'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Prostate'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf White Matter Lesions Segmentation V2.0] '''  
+
| 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" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]
+
| 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:Lupus3.png| 150px]]
+
| style="background:#CCFF99; color:black" align="center"|[[Image:ProstatePlanningOverview.png | 250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Orbit Segmentation'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''IGT'''
| style="background:#CCFF99; color:black" | '''[[Media:OrbitSegmentationTutorial.pdf‎| Segmentation of the Orbit ]]'''  
+
| 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" | [[Media:OrbiteSegmentationData.zip‎ ‎| Orbit Segmentation Data ]]
+
| 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:OrbitSegmentationt.png |250px]]  
+
| style="background:#CCFF99; color:black" align="center"| [[Image:300px-IGTBasicNavigationSummary.png| 250px]]
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''VMTK'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Orbit Segmentation'''
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf VMTK Coronary Arteries Centrelines Extraction]'''  
+
| style="background:#CCFF99; color:black" valign="top"| [[Media:OrbitSegmentationTutorial.pdf‎| '''Segmentation of the Orbit''']]
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/images/a/aa/TutorialVMTKCoronariesCenterlinesMRI_Data_Winter2010AHM.zip VMTK Centrelines Data]
+
| style="background:#CCFF99; color:black"  valign="top"| [[Media:OrbiteSegmentationData.zip‎ ‎| Orbit Segmentation Data ]]
| style="background:#CCFF99; color:black" align="Center"| [[Image:Vmtkcloseupvoronoicenterlinewithreference.png|250px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:OrbitSegmentationt.png |250px]]  
 
|-
 
|-
| style="background:#849f66; color:#3b3f33; font-size:110%" align="Center"| <span id="1.1"></span> '''Fiber Clustering'''
 
| style="background:#CCFF99; color:black" | '''[http://www.na-mic.org/Wiki/index.php/File:FiberClusteringTrainingTutorial_Winter2010AHM.pdf‎| EM Fiber Clustering ]'''
 
| style="background:#CCFF99; color:black" | [http://www.nitrc.org/projects/quantitativedti/‎ ‎ EM Fiber Clustering Data ]
 
| style="background:#CCFF99; color:black" align="Center"| [[Image:Shot2.png |250px]]
 
 
|}
 
|}
  
Line 166: Line 173:
  
  
{| border="1" cellpadding="5"
+
{| border="1" cellpadding="5" width="1000px"
 
|- style="background:#547389; color:#994139; font-size:130%" align="center"  
 
|- style="background:#547389; color:#994139; font-size:130%" align="center"  
| style="width:8%" ;align="Center"| '''Contest'''
+
|'''Contest'''
| style="width:40%" ;align="Center"| '''Tutorial'''
+
|'''Tutorial'''
| style="width:40%" ;align="Center"| '''Sample Data'''  
+
|'''Sample Data'''
| style="width:12%" ;align="Center"| '''Image'''
+
|'''Image'''
 
|-
 
|-
| style="background:#547389; color:#994139; font-size:110%" align="Center"| <span id="1.1"></span> '''Specialized'''
+
| style="background:#547389; color:#994139; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#b7cfd7; color:black" | '''[http://www.na-mic.org/Wiki/index.php/RobustStatisticsSegmentation‎ Robust Statistics Segmentation Tutorial]'''  
+
| 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" | [[Media:Patient1.tar.gz | '''Robust Statistics Segmentation dataset''']]
+
| 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]]
+
| style="background:#b7cfd7; color:black" align="center"| [[Image:RobustStatisticsSegmentation LiverSpleenKidney.png |250px]]
 
|-
 
|-
 
|}
 
|}

Latest revision as of 17:28, 30 January 2012

Home < Slicer3.4:Training

Slicer 3.4 Tutorials

  • For tutorials for other versions of Slicer, please visit the Slicer training portal.
  • 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).


Category Tutorial Sample Data Image
Basic Slicer3Minute Tutorial

The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.

Audience: First time users.
Slicer3Minute Data

The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
Slicer3Minute.PNG
Basic Slicer3 Manual Registration Tutorial

shows how to manually/interactively align two images in Slicer3.4 or 3.5

Audience: First time & early users.
Manual Registration Data

This dataset contains two brain MRI of a single subject, obtained in different orientations.
Slicer3 ManualRegistrationTutorial.gif
Core 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.
Slicer3Visualization Data

The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.
DataLoadingAndVisualization SPujol.png
Core 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.
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.
Programming
Specialized 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.
FreeSurfer Tutorial Data

The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
FreeSurferTutorial.PNG
Specialized 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.
Automatic Segmentation Data EMSegmentationTutorial.PNG
Specialized 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.
Atlas Merging Data (contains 2 full brain atlases + intermediate result files, 72MB) Slicer3 SurfaceRegistrationTutorial RegLib C11.gif
Specialized 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.
Neurosurgical Planning Data NeurosurgicalPlanningOverview.png
Specialized 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.
Diffusion Data Cc.PNG
Specialized 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.

Training Data download is integrated with the ChangeTracker module (see Tutorial) Slicer3.4.1-ChangeTracker.jpg
Specialized 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.

Liver Segmentation Data LiverSegmentation.png

Slicer Tutorial Contest

The following tutorials were part of the January 2010 Slicer tutorial contest, June 2009 Slicer tutorial contest and January 2009 Slicer tutorial contest.

January 2010 Slicer Tutorial Contest

DBPs/Collaboration Tutorial Sample Data Image
Fiber Clustering EM Fiber Clustering ‎ EM Fiber Clustering Data Shot2.png
VMTK VMTK Coronary Arteries centerlines Extraction VMTK Centrelines Data Vmtkcloseupvoronoicenterlinewithreference.png

June 2009 Slicer Tutorial Contest

DBPs/Collaboration Tutorial Sample Data Image
Confocal Microscopy Confocal Microscopy Microscopy Confocal Data MicroscopyTutorial.png
Autism ARCTIC: Automatic Regional Cortical ThICkness ARCTIC Data Corticalthickness.png
Prostate Trans-rectal MR guided prostate biopsy MR-guided Prostate Biopsy Data TransRectalBiopsy.png
Schizophrenia Python Stochastic Tractography Module Stochastic Tractography Data StochasticTractographyTutorial2.png
Lupus White Matter Lesions Segmentation Lesion Segmentation Tutorial Data LupusTutorial2.PNG

January 2009 Slicer Tutorial Contest

DBPs/Collaboration Tutorial Sample Data Image
Automated FE Mesh IA FEMesh Tutorial Mesh Tutorial Example Data Femesh-in-trunk-120808.png
Alcohol and Stress Interaction Non-Human Primate Segmentation Tutorial Non-Human Primate Segmentation Data Non-HumanPrimateSegmentation.png
Prostate MR-guided Prostate Interventions MR Guided Prostate Interventions Data ProstatePlanningOverview.png
IGT Basic Navigation Tutorial Basic Navigation Data 300px-IGTBasicNavigationSummary.png
Orbit Segmentation Segmentation of the Orbit Orbit Segmentation Data OrbitSegmentationt.png

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.


Contest Tutorial Sample Data Image
Specialized Robust Statistics Segmentation Tutorial Robust Statistics Segmentation Data RobustStatisticsSegmentation LiverSpleenKidney.png

Software Installation

  • The 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 here. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.

Older Tutorials