Difference between revisions of "Slicer3.4:Training"

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= Software Installation =  
+
=Slicer 3.4 Tutorials=
  
*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.
+
* 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).
  
= 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.
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{| border="1" cellpadding="5" width="1000px"
 
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|- style="background:#FFD700; color:#4A2A0A; font-size:130%" align="center"
= Older Versions =
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| '''Category'''
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2 training page].
+
| '''Tutorial'''
*Visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2 training page].
+
| '''Sample Data'''
 
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| '''Image'''
= Slicer 3.4 Tutorials =
+
|-
 
+
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"|<span id="1.1"></span> '''Basic'''
* The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment to accomplish certain tasks.
+
| 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" 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
{| border="1" cellpadding="5"
+
| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3Minute.PNG|250px]]
|- style="background:#FFFF00; color:black" align="left"  
+
|-
| style="width:5%" ;align="Center"| '''Category'''
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| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"|<span id="1.1"></span> '''Basic'''
| style="width:35%" ;align="Center"| '''Tutorial'''
+
| 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="width:30%" ;align="Center"| '''Sample Data'''  
+
| 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="width:10%" ;align="Center"|  
+
| 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'''
 +
| 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" 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]]
 +
|-
 +
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Core'''
 +
| 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" 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]]
 
|-
 
|-
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Basic'''
+
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FFFE59; 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.   
+
| 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:#FFFE59; 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
+
| 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:#FFFE59; color:black" align="Center"| [[Image:Slicer3Minute.PNG|200px]]
+
| style="background:#FDFC6D; color:black" align="center"| [[Image:FreeSurferTutorial.PNG|250px]]
 
|-
 
|-
| style="background:#FFD700; color:black" align="Center"| <span id="1.2"></span> '''Core'''
+
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FFFE59; 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.
+
| 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:#FFFE59; 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.
+
| style="background:#FDFC6D; color:black" valign="top" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation Data''']]  
| style="background:#FFFE59; color:black" align="Center"| [[Image:DataLoadingAndVisualization_SPujol.png|200px]]
+
| style="background:#FDFC6D; color:black" align="center"| [[Image:EMSegmentationTutorial.PNG|250px]]
 
|-
 
|-
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Core'''
+
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FFFE59; 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.
+
| 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:#FFFE59; 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.
+
| 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:#FFFE59; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]
+
| style="background:#FDFC6D; color:black" align="center"| [[Image:Slicer3_SurfaceRegistrationTutorial_RegLib_C11.gif|250px]]
 
|-
 
|-
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''
+
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FFFE59; 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.   
+
| 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:#FFFE59; 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.
+
| style="background:#FDFC6D; color:black" valign="top" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning Data ''']]
| style="background:#FFFE59; color:black" align="Center"| [[Image:FreeSurferTutorial.PNG|200px]]
+
| style="background:#FDFC6D; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
 
|-
 
|-
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''
+
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FFFE59; 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.
+
| 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.  
| style="background:#FFFE59; color:black" | [[Media:AutomaticSegmentation.zip| '''Automatic Segmentation dataset ''']]<br><br>
+
| style="background:#FDFC6D; color:black" valign="top" | [[Media:DiffusionDataset.zip | '''Diffusion Data''']]  
| style="background:#FFFE59; color:black" align="Center"| [[Image:EMSegmentationTutorial.PNG|200px]]
+
| style="background:#FDFC6D; color:black" align="center"| [[Image:cc.PNG |250px]]
 
|-
 
|-
| style="background:#FFD700; color:black" align="Center"| <span id="1.1"></span> '''Specialized'''
+
| style="background:#FFD700; color:#4A2A0A; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| style="background:#FFFE59; 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.
+
| 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.
| style="background:#FFFE59; color:black" | [[Media:NeurosurgicalPlanningTutorialData.zip| '''Neurosurgical Planning dataset ''']]<br><br>
+
'''Audience:''' All users interested in longitudinal analysis of pathology.
| style="background:#FFFE59; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px]]
+
| 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"| <span id="1.1"></span> '''Specialized'''
 +
| 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.
 +
| 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 =
 
= Slicer Tutorial Contest =
  
'''(under construction)'''
+
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'''==
  
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].  
+
{| 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> '''Fiber Clustering'''
 +
| 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" 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"| <span id="1.1"></span> '''VMTK'''
 +
| 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" 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:Vmtkcloseupvoronoicenterlinewithreference.png|250px]]
 +
|}
  
 +
== '''June 2009 Slicer Tutorial Contest'''==
  
{| border="1" cellpadding="5"
+
{| border="1" cellpadding="5" width="1000px"
|- style="background:#CCFF66; color:black" align="left"  
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|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"  
| style="width:5%" ;align="Center"| '''Contest'''
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|'''DBPs/Collaboration'''
| style="width:35%" ;align="Center"| '''Tutorial'''
+
|'''Tutorial'''
| style="width:30%" ;align="Center"| '''Sample Data'''
+
|'''Sample Data'''
| style="width:10%" ;align="Center"| '''Image'''
+
|'''Image'''
 +
|-
 +
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''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:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''Autism'''
| style="background:#CCFF99; color:black" | '''[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.na-mic.org/Wiki/images/3/33/ARCTIC-Slicer3-Tutorial.pdf '''ARCTIC: Automatic Regional Cortical ThICkness''']
| style="background:#CCFF99; color:black" | [http://www.ccdb.ucsd.edu/index.shtm  Microscopy Confocal Dataset]
+
| style="background:#CCFF99; color:black" valign="top" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]
| style="background:#CCFF99; color:black" align="Center"| [[Image:MicroscopyTutorial.png| 200 px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:Corticalthickness.png| 250px ]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''
+
| 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:ARCTIC-Slicer3-Tutorial.pdf ARCTIC: Automatic Regional Cortical ThICkness V2.1] '''  
+
| 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.nitrc.org/projects/arctic/ ARCTIC Data]
+
| style="background:#CCFF99; color:black" valign="top" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR-guided Prostate Biopsy Data]]
| style="background:#CCFF99; color:black" align="Center"| [[Image:Corticalthickness.png| 200 px ]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:TransRectalBiopsy.png| 250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''
+
| 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/0/06/DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf ‎Trans-rectal MR guided prostate biopsy] '''  
+
| style="background:#CCFF99; color:black" valign="top" | [[media:Stochastic_June09_3.ppt| '''Python Stochastic Tractography Module''']]
| style="background:#CCFF99; color:black" | [[Media:TransRectalProstateBiopsyTutorialDataset.zip| MR guided prostate biopsy Dataset]]
+
| 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:TransRectalBiopsy.png| 200 px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:StochasticTractographyTutorial2.png|250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''
+
| 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/index.php/File:Stochastic_June09_1.ppt Python Stochastic Tractography Module] '''  
+
| 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.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:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png|200 px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:LupusTutorial2.PNG| 250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Summer 2009'''
+
|}
| 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" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]
+
== '''January 2009 Slicer Tutorial Contest'''==
| style="background:#CCFF99; color:black" align="Center"| [[Image:LupusTutorial2.PNG| 200 px]]
+
 
 +
{| border="1" cellpadding="5" width="1000px"
 +
|- style="background:#849f66; color:#3b3f33; font-size:130%" align="center"
 +
|'''DBPs/Collaboration'''
 +
|'''Tutorial'''
 +
|'''Sample Data'''
 +
|'''Image'''
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
| 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/images/b/b8/IA-FEMesh-Tutorial-Notes.pdf IA FEMesh Tutorial] '''  
+
| 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:MeshTutorialExampleData.zip Mesh Tutorial Example 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:Femesh-in-trunk-120808.png |200px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:Femesh-in-trunk-120808.png|250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
| 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/8/83/EMSegment_TrainingTutorial.pdf Non-Human Primate Segmentation Tutorial] '''  
+
| 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.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Non-Human Primate Segmentation 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: Non-HumanPrimateSegmentation.png|200 px]]
+
| style="background:#CCFF99; color:black" align="center"| ‎[[Image: Non-HumanPrimateSegmentation.png|250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
| 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"  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:MRGuidedProstateInterventions.zip MR Guided Prostate Interventions 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:ProstatePlanningOverview.jpg | 200 px]]
+
| style="background:#CCFF99; color:black" align="center"|[[Image:ProstatePlanningOverview.png | 250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
| style="background:#849f66; color:#3b3f33; font-size:110%" align="center"| <span id="1.1"></span> '''IGT'''
| style="background:#CCFF99; color:black" | '''[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/Wiki/index.php/IGT:ToolKit/Navigation-tutorial '''Basic Navigation Tutorial''']
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/publications/item/view/1265 Basic Navigation 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:300px-IGTBasicNavigationSummary.png| 200 px]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:300px-IGTBasicNavigationSummary.png| 250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
| 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/index.php/Python_Stochastic_Tractography_Tutorial Python Stochastic Tractography Tutorial V1.0] '''  
+
| 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/index.php/File:IJdata.tar.gz Stochastic Tractography Data]
+
| style="background:#CCFF99; color:black"  valign="top"| [[Media:OrbiteSegmentationData.zip‎ ‎| Orbit Segmentation Data ]]
| style="background:#CCFF99; color:black" align="Center"| [[Image:StochasticTractographyTutorial2.png]]
+
| style="background:#CCFF99; color:black" align="center"| [[Image:OrbitSegmentationt.png |250px]]  
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
|}
| 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" | [http://www.nitrc.org/projects/arctic/ ARCTIC Data]
+
= Slicer 3.5 Tutorials=
| style="background:#CCFF99; color:black" align="Center"| [[Image:ArcticLogo.png‎| 200 px]]
+
 
 +
*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:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
| style="background:#547389; color:#994139; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized'''
| 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:#b7cfd7; color:black" valign="top"| [http://www.na-mic.org/Wiki/index.php/RobustStatisticsSegmentation‎ '''Robust Statistics Segmentation Tutorial''']
| style="background:#CCFF99; color:black" | [http://www.na-mic.org/Wiki/index.php/File:LesionSegmentationTutorialData.zip Lesion Segmentation Tutorial Data]
+
| style="background:#b7cfd7; color:black" valign="top" | [[Media:Patient1.tar.gz | '''Robust Statistics Segmentation Data''']]
| style="background:#CCFF99; color:black" align="Center"| [[Image:Lupus3.png| 150 px]]
+
| style="background:#b7cfd7; color:black" align="center"| [[Image:RobustStatisticsSegmentation LiverSpleenKidney.png |250px]]
 
|-
 
|-
| style="background:#CCFF66; color:black" align="Center"| <span id="1.1"></span> '''Winter 2009'''
+
|}
| style="background:#CCFF99; color:black" | ''' Segmentation of the Orbit '''
+
 
| style="background:#CCFF99; color:black" | --
+
=Software Installation=  
| style="background:#CCFF99; color:black" align="Center"| [[Image:OrbitSegmentationt.png |200 px]]
+
*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].

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