Slicer Wiki - User contributions [en]

Slicer 3.6:Training

2010-10-25T18:10:20Z

Swallace: /* Summer 2010 Tutorial Contest Entries (under construction) */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.pdf | Slicer3Minute Tutorial-PDF]]''' '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.ppt | Slicer3Minute Tutorial-PPT]]''' 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:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf‎ ‎ | Slicer3Visualization Tutorial-PDF]]''' '''[[media:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.1.ppt‎ | Slicer3Visualization Tutorial-PPT]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginners 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:ProgrammingIntoSlicer3.6_SoniaPujol.pdf |Programming in Slicer3 Tutorial-PDF]]''' ''' [[media:ProgrammingIntoSlicer3.6_SoniaPujol.ppt |Programming in Slicer3 Tutorial-PPT]]''' The Programming in Slicer3 tutorial is an introduction to the integration of C++ 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 Python 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:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf‎ |Hello Python Tutorial]] The Hello Python tutorial is an introduction to the integration of Python stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloPython.zip‎ | '''HelloPython Plugin''']] The HelloPython tutorial dataset contains an MR scan of the brain and pre-computed xml and Python code for integrating the Hello Python plug-in to Slicer3.
| style="background:#FFFFCC; color:black" align="center"| [[Image:HelloPythonTutorial.PNG|200px|Programming]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf |Interactive Editor-PDF]] ''' '''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.ppt | Interactive Editor-PPT]]''' 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:ManualRegistration_Slicer3.6.pdf‎ | Manual Registration-PDF]] ''' '''[[media:ManualRegistration_Slicer3.6.ppt | Manual Registration-PPT]]''' 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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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-PDF]]''' '''[[Media:Slicer3.6-ChangeTrackerTutorial.ppt‎ | Change Tracker Tutorial-PPT]]''' 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]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ | FreeSurfer Course ]]''' The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
 '''Audience:''' All users
| style="background:#FFFFCC; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip FreeSurfer tutorial data ''']
| style="background:#FFFFCC; color:black" align="center|[[Image:FreeSurferTutorial.PNG|250px]]
|-
| style="background:#FFFFCC; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| [[media:SlicerNeurosurgeryTutorial-3.6.1.pdf| '''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:#FFFFCC; color:black" valign="top" | [[Media:Slicer-tutorial-neurosurgery_slicer3.6.1.zip| '''Neurosurgical Planning Data ''']]
| style="background:#FFFFCC; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=

The following tutorials were part of the [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials Summer 2010 Slicer Tutorial Contest].

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/7/70/Stochastic_tutorial_data_TutorialContestSummer2010.zip Stochastic Tractography]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Stochastic_tutorial_uncinate.JPG |200px]]
|-

|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/index.php/File:PerkStationModule_TutorialContestSummer2010.pdf PERK Station Module] '''Audience:''' All users and developers. (Note: Windows only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/36/PerkStationData_TutorialContestSummer2010.zip PERK Station Module]
| style="background:#FFFFFF ; color:black" align="center"| [[File:PERKStation.png |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.

File:PerkStationData TutorialContestSummer2010.zip

2010-10-25T18:09:38Z

Swallace:

File:PERKStation.png

2010-10-25T18:06:51Z

Swallace:

File:PerkStationModule TutorialContestSummer2010.pdf

2010-10-25T17:42:22Z

Swallace:

Slicer 3.6:Training

2010-10-24T15:41:45Z

Swallace: /* Summer 2010 Tutorial Contest Entries (under construction) */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.pdf | Slicer3Minute Tutorial-PDF]]''' '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.ppt | Slicer3Minute Tutorial-PPT]]''' 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:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf‎ ‎ | Slicer3Visualization Tutorial-PDF]]''' '''[[media:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.1.ppt‎ | Slicer3Visualization Tutorial-PPT]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginners 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:ProgrammingIntoSlicer3.6_SoniaPujol.pdf |Programming in Slicer3 Tutorial-PDF]]''' ''' [[media:ProgrammingIntoSlicer3.6_SoniaPujol.ppt |Programming in Slicer3 Tutorial-PPT]]''' The Programming in Slicer3 tutorial is an introduction to the integration of C++ 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 Python 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:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf‎ |Hello Python Tutorial]] The Hello Python tutorial is an introduction to the integration of Python stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloPython.zip‎ | '''HelloPython Plugin''']] The HelloPython tutorial dataset contains an MR scan of the brain and pre-computed xml and Python code for integrating the Hello Python plug-in to Slicer3.
| style="background:#FFFFCC; color:black" align="center"| [[Image:HelloPythonTutorial.PNG|200px|Programming]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf |Interactive Editor-PDF]] ''' '''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.ppt | Interactive Editor-PPT]]''' 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:ManualRegistration_Slicer3.6.pdf‎ | Manual Registration-PDF]] ''' '''[[media:ManualRegistration_Slicer3.6.ppt | Manual Registration-PPT]]''' 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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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-PDF]]''' '''[[Media:Slicer3.6-ChangeTrackerTutorial.ppt‎ | Change Tracker Tutorial-PPT]]''' 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]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ | FreeSurfer Course ]]''' The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
 '''Audience:''' All users
| style="background:#FFFFCC; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip FreeSurfer tutorial data ''']
| style="background:#FFFFCC; color:black" align="center|[[Image:FreeSurferTutorial.PNG|250px]]
|-
| style="background:#FFFFCC; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| [[media:SlicerNeurosurgeryTutorial-3.6.1.pdf| '''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:#FFFFCC; color:black" valign="top" | [[Media:Slicer-tutorial-neurosurgery_slicer3.6.1.zip| '''Neurosurgical Planning Data ''']]
| style="background:#FFFFCC; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=

The following tutorials were part of the [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials Summer 2010 Slicer Tutorial Contest].

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/7/70/Stochastic_tutorial_data_TutorialContestSummer2010.zip Stochastic Tractography]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Stochastic_tutorial_uncinate.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

2010-10-24T15:41:22Z

Swallace: /* Summer 2010 Tutorial Contest Entries (under construction) */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.pdf | Slicer3Minute Tutorial-PDF]]''' '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.ppt | Slicer3Minute Tutorial-PPT]]''' 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:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf‎ ‎ | Slicer3Visualization Tutorial-PDF]]''' '''[[media:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.1.ppt‎ | Slicer3Visualization Tutorial-PPT]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginners 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:ProgrammingIntoSlicer3.6_SoniaPujol.pdf |Programming in Slicer3 Tutorial-PDF]]''' ''' [[media:ProgrammingIntoSlicer3.6_SoniaPujol.ppt |Programming in Slicer3 Tutorial-PPT]]''' The Programming in Slicer3 tutorial is an introduction to the integration of C++ 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 Python 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:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf‎ |Hello Python Tutorial]] The Hello Python tutorial is an introduction to the integration of Python stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloPython.zip‎ | '''HelloPython Plugin''']] The HelloPython tutorial dataset contains an MR scan of the brain and pre-computed xml and Python code for integrating the Hello Python plug-in to Slicer3.
| style="background:#FFFFCC; color:black" align="center"| [[Image:HelloPythonTutorial.PNG|200px|Programming]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf |Interactive Editor-PDF]] ''' '''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.ppt | Interactive Editor-PPT]]''' 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:ManualRegistration_Slicer3.6.pdf‎ | Manual Registration-PDF]] ''' '''[[media:ManualRegistration_Slicer3.6.ppt | Manual Registration-PPT]]''' 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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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-PDF]]''' '''[[Media:Slicer3.6-ChangeTrackerTutorial.ppt‎ | Change Tracker Tutorial-PPT]]''' 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]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ | FreeSurfer Course ]]''' The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
 '''Audience:''' All users
| style="background:#FFFFCC; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip FreeSurfer tutorial data ''']
| style="background:#FFFFCC; color:black" align="center|[[Image:FreeSurferTutorial.PNG|250px]]
|-
| style="background:#FFFFCC; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| [[media:SlicerNeurosurgeryTutorial-3.6.1.pdf| '''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:#FFFFCC; color:black" valign="top" | [[Media:Slicer-tutorial-neurosurgery_slicer3.6.1.zip| '''Neurosurgical Planning Data ''']]
| style="background:#FFFFCC; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=

The following tutorials were part of the [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials Summer 2010 Slicer Tutorial Contest].

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/7/70/Stochastic_tutorial_data_TutorialContestSummer2010.zip Stochastic Tractography]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Stochastic_tutorial_uncinate.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

2010-10-24T15:41:02Z

Swallace: /* Summer 2010 Tutorial Contest Entries (under construction) */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.pdf | Slicer3Minute Tutorial-PDF]]''' '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.ppt | Slicer3Minute Tutorial-PPT]]''' 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:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf‎ ‎ | Slicer3Visualization Tutorial-PDF]]''' '''[[media:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.1.ppt‎ | Slicer3Visualization Tutorial-PPT]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginners 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:ProgrammingIntoSlicer3.6_SoniaPujol.pdf |Programming in Slicer3 Tutorial-PDF]]''' ''' [[media:ProgrammingIntoSlicer3.6_SoniaPujol.ppt |Programming in Slicer3 Tutorial-PPT]]''' The Programming in Slicer3 tutorial is an introduction to the integration of C++ 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 Python 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:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf‎ |Hello Python Tutorial]] The Hello Python tutorial is an introduction to the integration of Python stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloPython.zip‎ | '''HelloPython Plugin''']] The HelloPython tutorial dataset contains an MR scan of the brain and pre-computed xml and Python code for integrating the Hello Python plug-in to Slicer3.
| style="background:#FFFFCC; color:black" align="center"| [[Image:HelloPythonTutorial.PNG|200px|Programming]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf |Interactive Editor-PDF]] ''' '''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.ppt | Interactive Editor-PPT]]''' 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:ManualRegistration_Slicer3.6.pdf‎ | Manual Registration-PDF]] ''' '''[[media:ManualRegistration_Slicer3.6.ppt | Manual Registration-PPT]]''' 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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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-PDF]]''' '''[[Media:Slicer3.6-ChangeTrackerTutorial.ppt‎ | Change Tracker Tutorial-PPT]]''' 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]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ | FreeSurfer Course ]]''' The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
 '''Audience:''' All users
| style="background:#FFFFCC; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip FreeSurfer tutorial data ''']
| style="background:#FFFFCC; color:black" align="center|[[Image:FreeSurferTutorial.PNG|250px]]
|-
| style="background:#FFFFCC; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| [[media:SlicerNeurosurgeryTutorial-3.6.1.pdf| '''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:#FFFFCC; color:black" valign="top" | [[Media:Slicer-tutorial-neurosurgery_slicer3.6.1.zip| '''Neurosurgical Planning Data ''']]
| style="background:#FFFFCC; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=

The following tutorials were part of the [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials Summer 2010 Slicer Tutorial Contest].

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/7/70/Stochastic_tutorial_data_TutorialContestSummer2010.zip Stochastic Tractography]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Stochastic_tutorial_uncinate.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

2010-10-21T19:20:55Z

Swallace: /* Summer 2010 Tutorial Contest Entries (under construction) */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.pdf | Slicer3Minute Tutorial-PDF]]''' '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.ppt | Slicer3Minute Tutorial-PPT]]''' 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:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf‎ ‎ | Slicer3Visualization Tutorial-PDF]]''' '''[[media:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.1.ppt‎ | Slicer3Visualization Tutorial-PPT]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginners 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:ProgrammingIntoSlicer3.6_SoniaPujol.pdf |Programming in Slicer3 Tutorial-PDF]]''' ''' [[media:ProgrammingIntoSlicer3.6_SoniaPujol.ppt |Programming in Slicer3 Tutorial-PPT]]''' The Programming in Slicer3 tutorial is an introduction to the integration of C++ 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 Python 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:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf‎ |Hello Python Tutorial]] The Hello Python tutorial is an introduction to the integration of Python stand-alone programs outside of the Slicer3 source tree. '''Audience:''' Programmers and Engineers.
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloPython.zip‎ | '''HelloPython Plugin''']] The HelloPython tutorial dataset contains an MR scan of the brain and pre-computed xml and Python code for integrating the Hello Python plug-in to Slicer3.
| style="background:#FFFFCC; color:black" align="center"| [[Image:HelloPythonTutorial.PNG|200px|Programming]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf |Interactive Editor-PDF]] ''' '''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.ppt | Interactive Editor-PPT]]''' 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:ManualRegistration_Slicer3.6.pdf‎ | Manual Registration-PDF]] ''' '''[[media:ManualRegistration_Slicer3.6.ppt | Manual Registration-PPT]]''' 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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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-PDF]]''' '''[[Media:Slicer3.6-ChangeTrackerTutorial.ppt‎ | Change Tracker Tutorial-PPT]]''' 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]]
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:FreeSurferCourse_Slicer3.6_SoniaPujol.pdf‎ | FreeSurfer Course ]]''' The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
 '''Audience:''' All users
| style="background:#FFFFCC; color:black" valign="top" |'''[http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip FreeSurfer tutorial data ''']
| style="background:#FFFFCC; color:black" align="center|[[Image:FreeSurferTutorial.PNG|250px]]
|-
| style="background:#FFFFCC; color:#4A2A0A; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFCC; color:black" valign="top"| [[media:SlicerNeurosurgeryTutorial-3.6.1.pdf| '''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:#FFFFCC; color:black" valign="top" | [[Media:Slicer-tutorial-neurosurgery_slicer3.6.1.zip| '''Neurosurgical Planning Data ''']]
| style="background:#FFFFCC; color:black" align="center"| [[Image:NeurosurgicalPlanningOverview.png|250px]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=

The following tutorials were part of the [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials Summer 2010 Slicer Tutorial Contest].

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] '''Audience:''' All users and developers. (Note: Mac and Linux only.)
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/7/70/Stochastic_tutorial_data_TutorialContestSummer2010.zip Stochastic Tractography]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Stochastic_tutorial_uncinate.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.

File:Stochastic tutorial uncinate.JPG

2010-10-21T19:18:38Z

Swallace:

File:Stochastic tutorial data TutorialContestSummer2010.zip

2010-10-21T19:15:19Z

Swallace:

File:Stochastic Tractography TutorialContestSummer2010.pdf

2010-10-21T19:14:22Z

Swallace:

File:RSS TutorialContestSummer2010.pdf

2010-10-18T19:40:42Z

Swallace: uploaded a new version of "File:RSS TutorialContestSummer2010.pdf"

Robust Statistics Segmentation- Summer 2010 tutorial contest

Slicer3:Build Instructions

2010-10-08T22:23:37Z

Swallace: /* getbuildtest on linux */

= All-in-one Script to checkout and build Slicer3 =

To compile and build Slicer3, you need a set of development packages installed on your machine:
* [[Slicer3:Build_Instructions#getbuildtest_on_linux| pre-requisite material for Linux]]
* [[Slicer3:Build_Instructions#getbuildtest_on_Windows| pre-requisite material for Windows]]
* [[Slicer3:Build_Instructions#getbuildtest_on_Apple_Mac_OS_X |pre-requisite material for Mac]]

There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. (Click [[Slicer3:getbuildtest | here for background on getbuildtest]] and the experimental getbuildtest2 version).

= Building the 3.6 release =

For Linux and Mac, just do the following two commands. If you are a Windows user, you need to [[Slicer3:Build_Instructions_Windows#Open_cygwin_terminal_window | open a cygwin terminal window]] and type the commands in that window.

svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-6 Slicer3

./Slicer3/Scripts/getbuildtest.tcl

For Slicer 3.4 build instructions, please see
[http://www.slicer.org/slicerWiki/index.php?title=Slicer3:Build_Instructions&oldid=14059#Building_the_3.4_release|a previous version of this page].

= Building the latest development version =

svn co http://svn.slicer.org/Slicer3/trunk Slicer3

./Slicer3/Scripts/getbuildtest.tcl

Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.

= To run (all platforms): =

./Slicer3-build/Slicer3

Note: the whole build environment takes about 8G of disk space.

= Additional Information About getbuildtest and Building Slicer =

== Testing ==

Note also that getbuildtest will do an Experimental submission to the [http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with

getbuildtest.tcl -t ""

Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).

== What does getbuildtest.tcl do? ==

This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.

Specifically, getbuildtest does the following steps:

* Refreshes Slicer3 svn
* Runs Scripts/genlib.tcl which does the following for each of the support libraries
** does a cvs/svn checkout/update
** runs cmake with the correct settings for use with Slicer3
** runs make (or developer studio) to build the libraries
* Runs cmake on Slicer3
* Builds Slicer3
* Runs ctest on Slicer3
* (optionally) Runs CPack on Slicer3

== Usage ==

Usage:

usage: getbuildtest [options] [target]
[target] is determined automatically if not specified
[options] is one of the following:
--help : prints this message and exits
--clean : delete lib and build directories first
-t --test-type : CTest test target
--release : compile with optimization flags
--update : does a cvs/svn update on each lib
--pack : builds a distribution package (cpack)

== Errors from getbuildtest ==

You will need to have your firewall configured to allow access to cvs servers through port 2401. Also you need 8081 for submitting to the dashboard.

Other errors might mean you don't have all the build tools (see next section).

If you want to generate a log of the build process, you can use a command like the following:

# for csh/tcsh:
./Scripts/getbuildtest.tcl |& tee build.log
or
# for sh/bash:
./Scripts/getbuildtest.tcl 2>&1 | tee build.log

'''Windows:''' visual studio build messages do not go to stdout/stderr, but each build directory in Slicer3-lib will have a buildlog.txt file with the details.

== Debugging ==

Since slicer relies on shared libraries, the correct paths must be set up before the debugger can operate (this is accomplished with the [[Slicer3:Launcher|Slicer3 Launcher]] which is in the top level of Slicer3-build). The actual executable entry point (which should not be invoked directly by users) is ''Slicer3-build/bin/Slicer3-real''. The following steps create a shell that has the proper paths set up:
./Slicer3 --launch xterm &
Inside the newly launched window, you can run:
./bin/Slicer3-real
or you can run the debugger of your choice in the new window.

On windows (with rxvt installed via cygwin) the commands are:
./Slicer3 --launch rxvt &
and
./bin/Debug/Slicer3-real.exe

Other tools, such as performance analyzers, memory checkers, etc can also be used in the subshell. Using the launcher is a convenient way to set up the paths for the local build without needing to set any library paths on a system-wide basis. Note that this allows you to have several slicer builds in different directories without having them interfere with one another. The slicer launcher should also allow you to run slicer with it's own local path settings even if you have globally installed versions of VTK, ITK, tcl, python, etc.

More information is available at the links below:

* For information on using the launcher to debug with gdb, see: [http://www.na-mic.org/Wiki/index.php/Slicer3_Q&A_2008-11-18#Debugging]
* For debugging with Visual Studio, see: [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging]
* For debugging command line modules, see [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging]

Note you can also debug in XCode with similar methods, but you may need to manually copy the DYLD_LIBRARY_PATH into the project properties (XCode does not seem to inherit from its parent shell).

== Updating Your getbuildtest Build ==

There are a few options:

* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.

The following command for unix machines will update, build, and launch the latest Slicer3:

svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)

Note that on Windows you can also use the CMakeSetup.exe interface to CMake and then use Microsoft Visual Studio for debugging. You can use a command like the following in a cygwin shell to use the slicer launcher to start up visual studio with the correct environment to find the .dll files needed for debugging.

./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 8/Common7/IDE/devenv.exe --detach Slicer3.sln

== getbuildtest on linux ==

To compile Slicer3 and do development, be sure you have a complete set of development packages installed on your machine. The exact packages vary by distribution, but include:
* gcc
* gcc-c++
* libX11
* libX11-devel (libX11-dev on Ubuntu 7.04)
* libXt-devel (libXt-dev on Ubuntu)
* opengl/mesa (libgl1-mesa-dev on Ubuntu)
* glu (libglu1-mesa-dev on Ubuntu)

Ubuntu one line install:

sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev libXt-dev libxext-dev libgl1-mesa-dev libglu1-mesa-dev libncurses5-dev tcsh

Also, be sure you have OpenGL and the GLX extension to X working. To check the installation, it is usually enough to confirm that the command <pre>glxgears</pre> runs with no errors.

On occasion, you will encounter a build error relating to the loading of the shared libraries libsvn_fs_util-1.so.0, which are required for the numpy build process. This is due to having a subversion 1.4 or lower installed on your machine. Since this is an optional build in Slicer, you can try building Slicer using these alternatives:
*Turning off python support in the build settings (USE_PYTHON set to "OFF")
*Set the USE_SYSTEM_PYTHON to "true"

== getbuildtest on Windows ==

The script should work when run from a [[Slicer3:Build_Instructions_Windows#Open_cygwin_terminal_window | cygwin terminal window]] on a properly configured windows environment.

Current requirements are:
* Windows XP, Windows Vista, or Windows 7 operating system (note: ''Python is disabled by default for non-XP builds due to compilation issues'')
* Fast network connection, no firewalls blocking outbound connections (cvs and svn will connect to servers to get source code)
* The build directory shall be on an NTFS formatted disk (CMake and VTK will not work on a FAT formatted disk), with about About 10GB free disk space
* Microsoft Visual Studio with Visual C++ compiler installed
** Install all available service packs for Visual C++
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically (if they are not installed in the default location or you have multiple compiler versions installed, then you may need to edit slicer_variables.tcl to set the compiler installation path).
** Compiler version:
*** Developer Studio 9.0 2008 Visual C++ - this compiler is used to build Slicer3.5 development releases, there are no known limitations
*** Developer Studio 9.0 2008 Visual C++ Express (the free version from Microsoft) - [[Slicer3:Build_Instructions_Windows#Installing_Microsoft_Visual_Studio_Express | see detailed installation instructions here]].
**** Python will be disabled (only Visual Studio 2008 compiler supported by python 2.6).
*** Developer Studio 8.0 2005 Visual C++ - it can be used to build Slicer3.5 with the following limitations
**** Python will be disabled (only Visual Studio 2008 compiler supported by python 2.6).
**** The compiler randomly crashes during the build (there is no known fix for this problem, just a workround: in case of a crash restart the build)
*** Developer Studio 7.1 2003 and older - not tested and may not work
* [http://www.cygwin.com Cygwin] installed - [[Slicer3:Build_Instructions_Windows#Installing_Cygwin | see detailed installation instructions here]]
* [http://nsis.sourceforge.net/Download NSIS] installed (needed for installation package generation)
* '''Windows 7''' - if you experience random failures during the build process, replace Slicer3-lib/CMake-build with the contents of this zip file: http://www.cmake.org/files/dev/cmake-2.8.1.20100603-g3d1e8-win32-.zip to address these issues with earlier cmake versions: http://public.kitware.com/Bug/view.php?id=10790 and http://public.kitware.com/Bug/view.php?id=10793

Follow this link for [[Slicer3:Build_Instructions_Windows#Troubleshooting | common errors and troubleshooting on windows]].

== getbuildtest on Apple Mac OS X ==

For Mac OS 10.4.10 install the following from the OS disks (not installed by default on new machines):
* Xcode Tools (OS Disk 1, default window)
* X11: also on OS Disk 1, but you need to scroll down and find the Optional Installs installer and select X11 under Applications. See [http://porting.openoffice.org/mac/faq/installing/X11.html step-by-step instructions].
* X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg
* Subversion. Installation [http://downloads.open.collab.net/binaries.html options here]. Get the latest svn version for compatibility with the server and be sure your client includes SSL (so it can access https repositories).

Remember to run getbuildtest from an xterm so the tests can access the X server.

Note: The Apple X11 application on Mac OSX 10.5.x (Leopard) crashes frequently. We suggest you replace the default XX with [http://xquartz.macosforge.org/trac/wiki XQuartz].

== getbuildtest on Solaris ==

Collaboration with the University of Szeged in Hungary has resulted in a port of slicer3 to the current generation of the Oracle (formerly Sun) Solaris operating system. More information, including binary downloads, is available [[Slicer3:Solaris|at the Slicer3 Solaris page]].

== configuration options ==

The file Slicer3/slicer_variables.tcl includes configuration options for which versions of support libraries to use. You may want to change these for testing or to get access to new functionality.

These flags control the versions of code pulled from external repositories:

set ::Slicer3_TAG "http://svn.slicer.org/Slicer3/trunk"
set ::CMAKE_TAG "CMake-2-6"
set ::KWWidgets_TAG "Slicer-3-2"
set ::VTK_TAG "VTK-5-2"
set ::ITK_TAG ITK-3-6
set ::PYTHON_TAG "http://svn.python.org/projects/python/branches/release25-maint"

Other libraries, such as Tcl/Tk, teem, and curl, together with windows binaries for CMake and Tcl/Tk are mirrored for efficiency at http://svn.slicer.org/Slicer3-lib-mirrors.

For example, you may want a build against the ITK cvs head. Change the flag value and then run

getbuildtest.tcl --update

which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use the --clean option which will delete all build directories and rebuild.

== Changing version numbers ==

Click [[Slicer3:ChangingVersionsCheckList | here]] for the checklist of things to do when branching svn and creating a new Slicer release.

= Building with Qt =

If you start with an already built slicer, you can [[Qt_in_Slicer3#Building_Slicer_with_Qt| add Qt to the build]]. As of fall 2009 this is still very much a work in progress and the details are expected to change.

= Manual Build =

You can also build Slicer without using getbuildtest.tcl. For more information about manually compiling Slicer, see [[Slicer3:Manual_Build|this page]].

= SBuild =

SBuild is a new, experimental build system for Slicer. For more information about SBuild, see [[Slicer3:SBuild|the SBuild page]].

Slicer3:Build Instructions

2010-10-08T22:20:27Z

Swallace: /* getbuildtest on linux */

= All-in-one Script to checkout and build Slicer3 =

To compile and build Slicer3, you need a set of development packages installed on your machine:
* [[Slicer3:Build_Instructions#getbuildtest_on_linux| pre-requisite material for Linux]]
* [[Slicer3:Build_Instructions#getbuildtest_on_Windows| pre-requisite material for Windows]]
* [[Slicer3:Build_Instructions#getbuildtest_on_Apple_Mac_OS_X |pre-requisite material for Mac]]

There's a script called getbuildtest.tcl that makes the support libraries (VTK, ITK, teem, etc) and also builds slicer and does a dashboard submission. (Click [[Slicer3:getbuildtest | here for background on getbuildtest]] and the experimental getbuildtest2 version).

= Building the 3.6 release =

For Linux and Mac, just do the following two commands. If you are a Windows user, you need to [[Slicer3:Build_Instructions_Windows#Open_cygwin_terminal_window | open a cygwin terminal window]] and type the commands in that window.

svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-6 Slicer3

./Slicer3/Scripts/getbuildtest.tcl

For Slicer 3.4 build instructions, please see
[http://www.slicer.org/slicerWiki/index.php?title=Slicer3:Build_Instructions&oldid=14059#Building_the_3.4_release|a previous version of this page].

= Building the latest development version =

svn co http://svn.slicer.org/Slicer3/trunk Slicer3

./Slicer3/Scripts/getbuildtest.tcl

Note: that a Slicer3-lib and Slicer3-build directory will be created for you. This is meant to be used to set up new machines and to run nightly testing of the full builds.

= To run (all platforms): =

./Slicer3-build/Slicer3

Note: the whole build environment takes about 8G of disk space.

= Additional Information About getbuildtest and Building Slicer =

== Testing ==

Note also that getbuildtest will do an Experimental submission to the [http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 dashboard]. If you want to use getbuildtest without submitting to the dashboard, you can set the test type to nothing with

getbuildtest.tcl -t ""

Other options for the -t (--test-type) option are Nightly or Continuous (or any of the [http://www.cmake.org/Wiki/CMake_Testing_With_CTest CTest] options).

== What does getbuildtest.tcl do? ==

This script just automates the steps needed to build slicer. What you end up with is a set of source and build directories that can either be further manipulated with getbuildtest or can be worked with normally. That is, on windows you will have solution files that you can load in visual studio for debugging and further development.

Specifically, getbuildtest does the following steps:

* Refreshes Slicer3 svn
* Runs Scripts/genlib.tcl which does the following for each of the support libraries
** does a cvs/svn checkout/update
** runs cmake with the correct settings for use with Slicer3
** runs make (or developer studio) to build the libraries
* Runs cmake on Slicer3
* Builds Slicer3
* Runs ctest on Slicer3
* (optionally) Runs CPack on Slicer3

== Usage ==

Usage:

usage: getbuildtest [options] [target]
[target] is determined automatically if not specified
[options] is one of the following:
--help : prints this message and exits
--clean : delete lib and build directories first
-t --test-type : CTest test target
--release : compile with optimization flags
--update : does a cvs/svn update on each lib
--pack : builds a distribution package (cpack)

== Errors from getbuildtest ==

You will need to have your firewall configured to allow access to cvs servers through port 2401. Also you need 8081 for submitting to the dashboard.

Other errors might mean you don't have all the build tools (see next section).

If you want to generate a log of the build process, you can use a command like the following:

# for csh/tcsh:
./Scripts/getbuildtest.tcl |& tee build.log
or
# for sh/bash:
./Scripts/getbuildtest.tcl 2>&1 | tee build.log

'''Windows:''' visual studio build messages do not go to stdout/stderr, but each build directory in Slicer3-lib will have a buildlog.txt file with the details.

== Debugging ==

Since slicer relies on shared libraries, the correct paths must be set up before the debugger can operate (this is accomplished with the [[Slicer3:Launcher|Slicer3 Launcher]] which is in the top level of Slicer3-build). The actual executable entry point (which should not be invoked directly by users) is ''Slicer3-build/bin/Slicer3-real''. The following steps create a shell that has the proper paths set up:
./Slicer3 --launch xterm &
Inside the newly launched window, you can run:
./bin/Slicer3-real
or you can run the debugger of your choice in the new window.

On windows (with rxvt installed via cygwin) the commands are:
./Slicer3 --launch rxvt &
and
./bin/Debug/Slicer3-real.exe

Other tools, such as performance analyzers, memory checkers, etc can also be used in the subshell. Using the launcher is a convenient way to set up the paths for the local build without needing to set any library paths on a system-wide basis. Note that this allows you to have several slicer builds in different directories without having them interfere with one another. The slicer launcher should also allow you to run slicer with it's own local path settings even if you have globally installed versions of VTK, ITK, tcl, python, etc.

More information is available at the links below:

* For information on using the launcher to debug with gdb, see: [http://www.na-mic.org/Wiki/index.php/Slicer3_Q&A_2008-11-18#Debugging]
* For debugging with Visual Studio, see: [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging]
* For debugging command line modules, see [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging]

Note you can also debug in XCode with similar methods, but you may need to manually copy the DYLD_LIBRARY_PATH into the project properties (XCode does not seem to inherit from its parent shell).

== Updating Your getbuildtest Build ==

There are a few options:

* you can re-run getbuildtest and it will update slicer3 and rebuild (just slicer3)
* you can add the --update option and all the libs will get a cvs/svn update and will rebuild if needed (good for tracking the development head of VTK/ITK/KWWidgets etc).
* you can just 'svn update' in the Slicer3 directory and then do 'make' in the Slicer3-build to get just the latest Slicer3 code.

The following command for unix machines will update, build, and launch the latest Slicer3:

svn update && (cd ../Slicer3-build; make && ./bin/Slicer3)

Note that on Windows you can also use the CMakeSetup.exe interface to CMake and then use Microsoft Visual Studio for debugging. You can use a command like the following in a cygwin shell to use the slicer launcher to start up visual studio with the correct environment to find the .dll files needed for debugging.

./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 8/Common7/IDE/devenv.exe --detach Slicer3.sln

== getbuildtest on linux ==

To compile Slicer3 and do development, be sure you have a complete set of development packages installed on your machine. The exact packages vary by distribution, but include:
* gcc
* gcc-c++
* libX11
* libX11-devel (libX11-dev on Ubuntu 7.04)
* libXt-devel (libXt-dev on Ubuntu)
* opengl/mesa (libgl1-mesa-dev on Ubuntu)
* glu (libglu1-mesa-dev on Ubuntu)

Ubuntu one line install:

sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev libXt-dev libxext-dev libgl1-mesa-dev libglu1-mesa-dev libncurses5-dev tcsh

Also, be sure you have OpenGL and the GLX extension to X working. To check the installation, it is usually enough to confirm that the command <pre>glxgears</pre> runs with no errors.

On occasion, you will encounter a build error relating to loading to the shared libraries libsvn_fs_util-1.so.0, which are required for the numpy build process. This is due to needing subversion 1.5 or higher installed. Since this is an optional build in Slicer, you can try building Slicer, using these alternatives:
*Turning off python support in the build settings
*Set the USE_SYSTEM_PYTHON to "true"

== getbuildtest on Windows ==

The script should work when run from a [[Slicer3:Build_Instructions_Windows#Open_cygwin_terminal_window | cygwin terminal window]] on a properly configured windows environment.

Current requirements are:
* Windows XP, Windows Vista, or Windows 7 operating system (note: ''Python is disabled by default for non-XP builds due to compilation issues'')
* Fast network connection, no firewalls blocking outbound connections (cvs and svn will connect to servers to get source code)
* The build directory shall be on an NTFS formatted disk (CMake and VTK will not work on a FAT formatted disk), with about About 10GB free disk space
* Microsoft Visual Studio with Visual C++ compiler installed
** Install all available service packs for Visual C++
** If they are installed in the default locations in "c:/Program Files" they will be detected by the build script automatically (if they are not installed in the default location or you have multiple compiler versions installed, then you may need to edit slicer_variables.tcl to set the compiler installation path).
** Compiler version:
*** Developer Studio 9.0 2008 Visual C++ - this compiler is used to build Slicer3.5 development releases, there are no known limitations
*** Developer Studio 9.0 2008 Visual C++ Express (the free version from Microsoft) - [[Slicer3:Build_Instructions_Windows#Installing_Microsoft_Visual_Studio_Express | see detailed installation instructions here]].
**** Python will be disabled (only Visual Studio 2008 compiler supported by python 2.6).
*** Developer Studio 8.0 2005 Visual C++ - it can be used to build Slicer3.5 with the following limitations
**** Python will be disabled (only Visual Studio 2008 compiler supported by python 2.6).
**** The compiler randomly crashes during the build (there is no known fix for this problem, just a workround: in case of a crash restart the build)
*** Developer Studio 7.1 2003 and older - not tested and may not work
* [http://www.cygwin.com Cygwin] installed - [[Slicer3:Build_Instructions_Windows#Installing_Cygwin | see detailed installation instructions here]]
* [http://nsis.sourceforge.net/Download NSIS] installed (needed for installation package generation)
* '''Windows 7''' - if you experience random failures during the build process, replace Slicer3-lib/CMake-build with the contents of this zip file: http://www.cmake.org/files/dev/cmake-2.8.1.20100603-g3d1e8-win32-.zip to address these issues with earlier cmake versions: http://public.kitware.com/Bug/view.php?id=10790 and http://public.kitware.com/Bug/view.php?id=10793

Follow this link for [[Slicer3:Build_Instructions_Windows#Troubleshooting | common errors and troubleshooting on windows]].

== getbuildtest on Apple Mac OS X ==

For Mac OS 10.4.10 install the following from the OS disks (not installed by default on new machines):
* Xcode Tools (OS Disk 1, default window)
* X11: also on OS Disk 1, but you need to scroll down and find the Optional Installs installer and select X11 under Applications. See [http://porting.openoffice.org/mac/faq/installing/X11.html step-by-step instructions].
* X11SDK - from OS Disk 1, Xcode Tools/Packages/X11SDK.pkg
* Subversion. Installation [http://downloads.open.collab.net/binaries.html options here]. Get the latest svn version for compatibility with the server and be sure your client includes SSL (so it can access https repositories).

Remember to run getbuildtest from an xterm so the tests can access the X server.

Note: The Apple X11 application on Mac OSX 10.5.x (Leopard) crashes frequently. We suggest you replace the default XX with [http://xquartz.macosforge.org/trac/wiki XQuartz].

== getbuildtest on Solaris ==

Collaboration with the University of Szeged in Hungary has resulted in a port of slicer3 to the current generation of the Oracle (formerly Sun) Solaris operating system. More information, including binary downloads, is available [[Slicer3:Solaris|at the Slicer3 Solaris page]].

== configuration options ==

The file Slicer3/slicer_variables.tcl includes configuration options for which versions of support libraries to use. You may want to change these for testing or to get access to new functionality.

These flags control the versions of code pulled from external repositories:

set ::Slicer3_TAG "http://svn.slicer.org/Slicer3/trunk"
set ::CMAKE_TAG "CMake-2-6"
set ::KWWidgets_TAG "Slicer-3-2"
set ::VTK_TAG "VTK-5-2"
set ::ITK_TAG ITK-3-6
set ::PYTHON_TAG "http://svn.python.org/projects/python/branches/release25-maint"

Other libraries, such as Tcl/Tk, teem, and curl, together with windows binaries for CMake and Tcl/Tk are mirrored for efficiency at http://svn.slicer.org/Slicer3-lib-mirrors.

For example, you may want a build against the ITK cvs head. Change the flag value and then run

getbuildtest.tcl --update

which will get the version from cvs, build it, and rebuild slicer3. Depending on how radically different the versions you build are, you may need to use the --clean option which will delete all build directories and rebuild.

== Changing version numbers ==

Click [[Slicer3:ChangingVersionsCheckList | here]] for the checklist of things to do when branching svn and creating a new Slicer release.

= Building with Qt =

If you start with an already built slicer, you can [[Qt_in_Slicer3#Building_Slicer_with_Qt| add Qt to the build]]. As of fall 2009 this is still very much a work in progress and the details are expected to change.

= Manual Build =

You can also build Slicer without using getbuildtest.tcl. For more information about manually compiling Slicer, see [[Slicer3:Manual_Build|this page]].

= SBuild =

SBuild is a new, experimental build system for Slicer. For more information about SBuild, see [[Slicer3:SBuild|the SBuild page]].

File:Slicer-tutorial-neurosurgery.zip

2010-09-15T06:10:05Z

Swallace: uploaded a new version of "File:Slicer-tutorial-neurosurgery.zip": Revised zip file for neurosurgery tutorial using Nicole's baseline-noseedingparameters.mrml file to replace the original baseline.mrml file.

File:SlicerNeurosurgeryTutorial-3.6.1.ppt

2010-09-15T06:08:27Z

Swallace:

File:ProgrammingIntoSlicer3.6 Python SoniaPujol.pdf

2010-09-01T18:18:42Z

Swallace:

Slicer 3.6:Training

2010-09-01T16:20:45Z

Swallace: /* Slicer 3.6 Tutorials */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| '''Core'''
| style="background:#FFFFCC; color:black" valign="top"| '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.pdf | Slicer3Minute Tutorial-PDF]]''' '''[[Media:Slicer3Minute_SoniaPujol_3.6.1.ppt | Slicer3Minute Tutorial-PPT]]''' 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:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf‎ ‎ | Slicer3Visualization Tutorial-PDF]]''' '''[[media:Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.1.ppt‎ | Slicer3Visualization Tutorial-PPT]]''' The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. '''Audience:''' All beginners 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:ProgrammingIntoSlicer3.6_SoniaPujol.pdf |Programming in Slicer3 Tutorial-PDF]]''' ''' [[media:ProgrammingIntoSlicer3.6_SoniaPujol.ppt |Programming in Slicer3 Tutorial-PPT]]''' 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_Slicer3.6_SoniaPujol.pdf |Interactive Editor-PDF]] ''' '''[[media:InteractiveEditorTutorial_Slicer3.6_SoniaPujol.ppt | Interactive Editor-PPT]]''' 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:ManualRegistration_Slicer3.6.pdf‎ | Manual Registration-PDF]] ''' '''[[media:ManualRegistration_Slicer3.6.ppt | Manual Registration-PPT]]''' 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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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-PDF]]''' '''[[Media:Slicer3.6-ChangeTrackerTutorial.ppt‎ | Change Tracker Tutorial-PPT]]''' 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]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=
* [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials See here]

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |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.

File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.1.ppt

2010-09-01T16:17:02Z

Swallace:

File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt

2010-09-01T16:14:38Z

Swallace: uploaded a new version of "File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt": Revised version of tutorial with monor slide edits to slide 1. Otherwise, content the same.

File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt

2010-09-01T16:10:09Z

Swallace: uploaded a new version of "File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt"

File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt

2010-09-01T16:05:23Z

Swallace: uploaded a new version of "File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt"

File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt

2010-09-01T15:52:26Z

Swallace: uploaded a new version of "File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.ppt"

File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.pdf

2010-09-01T15:51:29Z

Swallace: uploaded a new version of "File:Slicer3 DataLoadingAndVisualization SoniaPujol3.6.pdf"

Slicer 3.6:Training

Slicer 3.6:Training

2010-08-09T11:37:09Z

Swallace: /* Slicer 3.6 Tutorials */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''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 beginners 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 |Interactive 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:ManualRegistration_Slicer3.6.pdf‎ | Manual Registration-PDF]] ''' 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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=
* [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials See here]

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |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.

File:ManualRegistration Slicer3.6.pdf

2010-08-09T11:35:46Z

Swallace:

File:ManualRegistration 3.6 noGIF.pdf

2010-08-09T11:29:37Z

Swallace: uploaded a new version of "File:ManualRegistration 3.6 noGIF.pdf"

Manual Registration tutorial pdf with minor edits on page 4.

Slicer 3.6:Training

2010-08-09T11:25:01Z

Swallace: /* Slicer 3.6 Tutorials */

=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="3" width="1000px"
|- style="background:#CCFF99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''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 beginners 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 |Interactive 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:ManualRegistration 3.6 noGIF.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/images/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_Slicer3.6.1_SoniaPujol_Aug2010.pdf‎ | Diffusion MRI tutorial-PDF]]''' '''[[Media:DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.ppt‎ |Diffusion MRI tutorial-PPT]]''' 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]]
|}

=Summer 2010 Tutorial Contest Entries (under construction)=
* [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials See here]

{| border="1" cellpadding="3" width="1000px"
|- style="background:#FFCC99; color:black; font-size:130%" align="center"
|style="width:100px"|'''Category'''
|style="width:350px"|'''Tutorial'''
|style="width:350px"|'''Sample Data'''
|style="width:200px"|'''Image'''
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data] 
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]]
|-
| style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:LongitudinalLesionComparison2_TutorialContestSummer2010.zip Longitudinal Lesion Comparison Data]
| style="background:#FFFFFF ; color:black" align="center"| [[File:Longitudinal_Lesion.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/3/3a/ProstateNavData_TutorialContestSummer2010.zip Robot-Assisted MRI-Guided Prostate Biopsy]
| style="background:#FFFFFF ; color:black" align="center"| [[File:ProstateNav.png |200px]]
|-
|style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| '''Specialized'''
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] '''Audience:''' All users and developers.
| style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration]
| style="background:#FFFFFF ; color:black" align="center"| [[File:AtlasLabelFusion.png |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.

File:DiffusionMRITutorial Slicer3.6.1 SoniaPujol Aug2010.ppt

2010-08-09T11:22:05Z

Swallace: Ppt slides for DTI tutorial with edits for Slicer3.6.1

Ppt slides for DTI tutorial with edits for Slicer3.6.1