Difference between revisions of "Slicer3.4:Training"
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Revision as of 18:22, 5 May 2010
Home < Slicer3.4:TrainingContents
Slicer 3.4 Tutorials
- The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.4) to accomplish certain tasks.
- For questions related to the Slicer3.4 Compendium, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
Category | Tutorial | Sample Data | Image |
Basic | Slicer3Minute Tutorial The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4. Audience: First time users. |
Slicer3Minute dataset The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy |
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Basic | Slicer3 Manual Registration Tutorial shows how to manually/interactively align two images in Slicer3.4 or 3.5 Audience: First time & early users. |
Manual Registration example dataset This dataset contains two brain MRI of a single subject, obtained in different orientations. |
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Core | Slicer3Visualization Tutorial The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4. Audience: All beginning users including clinicians, scientists, engineers and programmers. |
Slicer3Visualization dataset The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy. |
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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. |
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Specialized | 3D Visualization of FreeSurfer Data The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4. Audience: All users. |
FreeSurfer Tutorial dataset The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions. |
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Specialized | Automatic Segmentation Tutorial The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data. Audience: Programmers and Engineers. |
Automatic Segmentation dataset | |
Specialized | Atlas Label Merging & Surface Based Registration Tutorial This tutorial guides through the creation and co-registration of surface models of atlas structures (thalamus & thalamic nuclei) and subsequent merging of two labelmaps. |
Atlas Merging tutorial dataset (contains 2 full brain atlases + intermediate result files, 72MB) | |
Specialized | Neurosurgical Planning Tutorial This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules. Audience: All users interested in image-guided therapy. |
Neurosurgical Planning dataset | |
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 dataset | |
Specialized | ChangeTracker Tutorial This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans. Audience: All users interested in longitudinal analysis of pathology. |
Training data download is integrated with the ChangeTracker module (see Tutorial) | |
Specialized | LiverSegmentation Tutorial This tutorial introduces translational clinical scientists to the capabilities of the 3D Slicer software through the segmentation of the liver. Audience: All users and developers. |
Liver Segmentation dataset |
Slicer Tutorial Contest
The following tutorials were part of the June 2009 Slicer tutorial contest and January 2009 Slicer tutorial contest.
June 2009 Slicer Tutorial Contest
Driving Biological Project/Collaboration | Tutorial | Sample Data | Image |
Confocal Microscopy | Confocal Microscopy | Microscopy Confocal Dataset | |
Autism | ARCTIC: Automatic Regional Cortical ThICkness V2.1 | ARCTIC Data | |
Prostate | Trans-rectal MR guided prostate biopsy | MR guided prostate biopsy Dataset | |
Schizophrenia | Python Stochastic Tractography Module | Stochastic Tractography Data | |
Lupus | White Matter Lesions Segmentation V2.2 | Lesion Segmentation Tutorial Data |
January 2009 Slicer tutorial contest
Driving Biological Project/Collaboration | Tutorial | Sample Data | Image |
Automated FE Mesh | IA FEMesh Tutorial | Mesh Tutorial Example Data | |
Alcohol and Stress Interaction | Non-Human Primate Segmentation Tutorial | Non-Human Primate Segmentation Data | |
Prostate | MR Guided Prostate Interventions | MR Guided Prostate Interventions Data | |
IGT | Basic Navigation Tutorial | Basic Navigation Data | |
Orbit Segmentation | Segmentation of the Orbit | Orbit Segmentation Data | |
VMTK | VMTK Coronary Arteries Centrelines Extraction | VMTK Centrelines Data | |
Fiber Clustering | EM Fiber Clustering | EM Fiber Clustering Data |
Slicer 3.5 Tutorials
- The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.5) to accomplish certain tasks.
Contest | Tutorial | Sample Data | Image |
Specialized | Robust Statistics Segmentation Tutorial | Robust Statistics Segmentation dataset |
Software Installation
- The Slicer download page contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.
Software Documentation
- For the Slicer 3.4 manual pages please click here. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.
Older Tutorials
- Visit the Slicer 3.2 training page.
- Visit the Slicer 2 training page.