Difference between revisions of "Slicer 3.6:Training"
From Slicer Wiki
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− | {| border="1" cellpadding=" | + | {| border="1" cellpadding="3" width="1000px" |
− | |- style="background:# | + | |- style="background:#FFCC99; color:black; font-size:130%" align="center" |
− | |'''Category''' | + | |style="width:100px"|'''Category''' |
− | |'''Tutorial''' | + | |style="width:350px"|'''Tutorial''' |
− | |'''Sample Data''' | + | |style="width:350px"|'''Sample Data''' |
− | |'''Image''' | + | |style="width:200px"|'''Image''' |
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| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | | style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | ||
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| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | | style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | ||
− | | style="background:#FFFFCC; color:black" valign="top"| ''' [[media:ProgrammingIntoSlicer3_SoniaPujol.pdf |Programming in Slicer3 Tutorial]]'''<br><br>The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br><br>'''Audience:''' Programmers and Engineers. | + | | style="background:#FFFFCC; color:black" valign="top"|''' [[media:ProgrammingIntoSlicer3_SoniaPujol.pdf |Programming in Slicer3 Tutorial]]'''<br><br>The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.<br><br>'''Audience:''' Programmers and Engineers. |
| style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3. | | style="background:#FFFFCC; color:black" valign="top" | [[Media:HelloWorld_Plugin.zip| '''HelloWorld Plugin''']]<br><br> The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3. | ||
| style="background:#FFFFCC; color:black" align="center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]] | | style="background:#FFFFCC; color:black" align="center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]] | ||
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| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | | style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | ||
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_SoniaPujol.pdf |Interactive Editor]] ''' <br><br> Shows how to use the interactive editing tools in Slicer. <br>'''Audience:''' All users and developers. | | style="background:#FFFFCC; color:black" valign="top"|'''[[media:InteractiveEditorTutorial_SoniaPujol.pdf |Interactive Editor]] ''' <br><br> Shows how to use the interactive editing tools in Slicer. <br>'''Audience:''' All users and developers. | ||
− | | style="background:#FFFFCC; color:black" valign="top" | '''[http://www.slicer.org/slicerWiki/index.php/File:EditorTutorialDataset.zip Editor Data]'''<br><br>This dataset contains a MR dataset of the brain. | + | | style="background:#FFFFCC; color:black" valign="top"|'''[http://www.slicer.org/slicerWiki/index.php/File:EditorTutorialDataset.zip Editor Data]'''<br><br>This dataset contains a MR dataset of the brain. |
− | | style="background:#FFFFCC; color:black" align="center"| [[Image:InteractiveEditor.png|200px]] | + | | style="background:#FFFFCC; color:black" align="center"|[[Image:InteractiveEditor.png|200px]] |
|- | |- | ||
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | | style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Core''' | ||
| style="background:#FFFFCC; color:black" valign="top"|'''[[media:ManualRegistration 3.6 noGIF.pdf | Manual Registration]] ''' <br><br> Shows how to manually/interactively align two images in Slicer3.6 <br><br>'''Audience:''' First time & early users. | | style="background:#FFFFCC; color:black" valign="top"|'''[[media:ManualRegistration 3.6 noGIF.pdf | Manual Registration]] ''' <br><br> Shows how to manually/interactively align two images in Slicer3.6 <br><br>'''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]'''<br><br>This dataset contains two brain MRI of a single subject, obtained in different orientations. | + | | style="background:#FFFFCC; color:black" valign="top"|'''[http://www.slicer.org/slicerWiki/images/8/88/Slicer3_Tutorial_ManualRegistration_ExampleDataset.zip Manual Registration Data]'''<br><br>This dataset contains two brain MRI of a single subject, obtained in different orientations. |
− | | style="background:#FFFFCC; color:black" align="center"| [[Image:Slicer3_ManualRegistrationTutorial.gif|200px]] | + | | style="background:#FFFFCC; color:black" align="center"|[[Image:Slicer3_ManualRegistrationTutorial.gif|200px]] |
|- | |- | ||
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | | style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | ||
− | | style="background:#FFFFCC; color:black" valign="top"| '''[[media:DiffusionMRITutorial_Slicer3.6_SoniaPujol.pdf | Diffusion MRI Tutorial ]]''' <br><br>This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. <br><br>'''Audience:''' All users and developers. | + | | style="background:#FFFFCC; color:black" valign="top"|'''[[media:DiffusionMRITutorial_Slicer3.6_SoniaPujol.pdf | Diffusion MRI Tutorial ]]''' <br><br>This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. <br><br>'''Audience:''' All users and developers. |
− | | style="background:#FFFFCC; color:black" valign="top" |''' [http://www.slicer.org/slicerWiki/images/c/cf/DiffusionDataset.zip Diffusion Data]''' | + | | 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:black" align="center"|[[Image:cc.PNG |200px]] |
|- | |- | ||
| style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | | style="background:#FFFFCC; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | ||
− | | style="background:#FFFFCC; color:black" valign="top"| '''[[media:Slicer3.6-ChangeTrackerTutorial.pdf | Change Tracker Tutorial]]''' <br><br>This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans. <br><br>'''Audience:''' All users interested in longitudinal analysis of pathology. | + | | style="background:#FFFFCC; color:black" valign="top"|'''[[media:Slicer3.6-ChangeTrackerTutorial.pdf | Change Tracker Tutorial]]''' <br><br>This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans. <br><br>'''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" 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:black" align="center"|[[Image:Slicer3.4.1-ChangeTracker.jpg|200px]] |
|} | |} | ||
− | =Summer 2010 Tutorial Contest Entries ( under construction)= | + | =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] | * [http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest#List_of_submitted_tutorials See here] | ||
− | {| border="1" cellpadding=" | + | {| border="1" cellpadding="3" width="1000px" |
|- style="background:#FFCC99; color:black; font-size:130%" align="center" | |- style="background:#FFCC99; color:black; font-size:130%" align="center" | ||
− | |'''Category''' | + | |style="width:100px"|'''Category''' |
− | |'''Tutorial''' | + | |style="width:350px"|'''Tutorial''' |
− | |'''Sample Data''' | + | |style="width:350px"|'''Sample Data''' |
− | |'''Image''' | + | |style="width:200px"|'''Image''' |
|- | |- | ||
− | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | + | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span>'''Specialized''' |
| style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] <br><br> '''Audience:''' All users and developers. | | style="background:#FFFFFF color:black" valign="top"| [http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow tutorial] <br><br> '''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]<br><br> | | style="background:#FFFFFF ; color:black" valign="top" | [http://www.slicer.org/slicerWiki/index.php/File:IAFEMeshData-TutorialContestSummer2010.zip Meshing Workflow Data]<br><br> | ||
| style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]] | | style="background:#FFFFFF ; color:black" align="center"| [[File:FEMesh.png |200px]] | ||
|- | |- | ||
− | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | + | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span>'''Specialized''' |
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] <br><br>'''Audience:''' All users and developers. | | style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials tutorial] <br><br>'''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]<br><br> | | style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials Data]<br><br> | ||
| style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]] | | style="background:#FFFFFF ; color:black" align="center"| [[File:Fiducials.png |200px]] | ||
|- | |- | ||
− | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | + | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span>'''Specialized''' |
| style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] <br><br>'''Audience:''' All users and developers. | | style="background:#FFFFFF ; color:black" valign="top"| [http://wiki.slicer.org/slicerWiki/images/3/3c/RSS_TutorialContestSummer2010.pdf Robust Statistic Segmenter] <br><br>'''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]<br><br> | | style="background:#FFFFFF ; color:black" valign="top" | [http://wiki.na-mic.org/Wiki/index.php/File:RSSData_TutorialContestSummer2010.zip Robust Statistic Segmenter Data]<br><br> | ||
| style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]] | | style="background:#FFFFFF ; color:black" align="center"| [[File:RSS.png |200px]] | ||
|- | |- | ||
− | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | + | | style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span>'''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] <br><br>'''Audience:''' All users and developers. | | style="background:#FFFFFF ; color:black" valign="top"|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal lesion comparison] <br><br>'''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" 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:black" align="center"| [[File:Longitudinal_Lesion.png |200px]] | ||
|- | |- | ||
− | |style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | + | |style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span>'''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] <br><br>'''Audience:''' All users and developers. | | style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] <br><br>'''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" 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:black" align="center"| [[File:ProstateNav.png |200px]] | ||
|- | |- | ||
− | |style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span> '''Specialized''' | + | |style="background:#FFFFFF ; color:blue; font-size:110%" align="center"| <span id="1.1"></span>'''Specialized''' |
| style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] <br><br>'''Audience:''' All users and developers. | | style="background:#FFFFFF ; color:black" valign="top"|[http://www.slicer.org/slicerWiki/images/0/0a/LabelFusion_Tutorial.pdf Atlas Label Fusion & Surface Registration] <br><br>'''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" valign="top" | [http://www.slicer.org/slicerWiki/images/2/27/AtlasLabelFusion_TutorialContestSummer2010.zip Atlas Label Fusion & Surface Registration] |
Revision as of 15:08, 4 August 2010
Home < Slicer 3.6:TrainingContents
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 Slicer training portal.
- For questions related to the Slicer3 Compendium, please send an e-mail to Sonia Pujol, Ph.D
Category | Tutorial | Sample Data | Image |
Core | Slicer3Minute Tutorial The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.6. Audience: First time users. |
Slicer3Minute Data The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy |
|
Core | Slicer3Visualization Tutorial The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. Audience: All beginners including clinicians, scientists, engineers and programmers. |
Slicer3Visualization Data The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy. |
|
Core | Programming in Slicer3 Tutorial The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree. Audience: Programmers and Engineers. |
HelloWorld Plugin The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3. |
|
Core | Interactive Editor Shows how to use the interactive editing tools in Slicer. Audience: All users and developers. |
Editor Data This dataset contains a MR dataset of the brain. |
|
Core | Manual Registration Shows how to manually/interactively align two images in Slicer3.6 Audience: First time & early users. |
Manual Registration Data This dataset contains two brain MRI of a single subject, obtained in different orientations. |
|
Specialized | Diffusion MRI Tutorial This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. Audience: All users and developers. |
Diffusion Data | |
Specialized | 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. |
Training Data download is integrated with the ChangeTracker module (see Tutorial) |
Summer 2010 Tutorial Contest Entries (under construction)
Category | Tutorial | Sample Data | Image |
Specialized | Meshing Workflow tutorial Audience: All users and developers. |
Meshing Workflow Data |
|
Specialized | Fiducials tutorial Audience: All users and developers. |
Fiducials Data |
|
Specialized | Robust Statistic Segmenter Audience: All users and developers. |
Robust Statistic Segmenter Data |
|
Specialized | Longitudinal lesion comparison Audience: All users and developers. |
Longitudinal Lesion Comparison Data | |
Specialized | Robot-Assisted MRI-Guided Prostate Biopsy Audience: All users and developers. |
Robot-Assisted MRI-Guided Prostate Biopsy | |
Specialized | Atlas Label Fusion & Surface Registration Audience: All users and developers. |
Atlas Label Fusion & Surface Registration |
Software Installation
- The Slicer download page contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.
Software Documentation
- For the Slicer 3.6 manual pages please click here. These pages are the reference manual for Slicer 3.6 and briefly explain the functionality found in panels and modules.