SlicerMorph UCMP Workshop

Day 1: Friday April 16th

• Imaging concepts, overall review of tasks in 3D digital morphology
• Nut and bolts of working with Slicer
• Getting data in (Imagestacks and Morphosource)
• Visualization (Volume Rendering)
• Segmentation
• Building Models and exporting, sharing data/anatomy/segmentation
• Importance of preserving scale, format discussions.

Tutorials for Friday April 16th

• SlicerMorph Preferences (SlicerMorph Specific)

• Sample Data (Core Slicer module)

• ImageStacks (SlicerMorph Specific)

• DICOM (Core Slicer Module)

• ExportAs (SlicerMorph Specific)

• Volumes, Crop Volumes (Core Slicer modules)

• Volume Rendering (Core Slicer Module)

• Animator (SlicerMorph Specific)

• Segmentation

  • Segmentation Concepts

  • Segmentation Tutorial

• Working with 3D Models in Slicer

  • Models (Core Slicer Module)

  • Surface Toolbox, Dynamic Modeler (Core Slicer Module)

• Transforms Core Slicer Module

Day 2: Friday April 23rd

Concepts to cover: (Links takes you to the module descriptions and documentation. )

• Recap from Day 1 (Import->Visualize->Segment pipeline, a few segmentation recipes, keyboard short-cuts etc).
• Very brief presentation on GMM concepts
• Measurements (lengths, angles, areas) and Landmarks via Markups module
• Curve-based and patch-based semi-landmarking
• Transfering semiLMs to new samples via PlaceSemiLMPatches or ProjectSemiLMs
• PseudoLMGenerator: How to create pseudo-landmark templates
• MarkupEditor (to retouch pseudoLMs and others)
• MergeMarkups (to join fixed and semiLMs into a single markup node)
• GPA module in SlicerMorph

Tutorials for Friday April 23rd

• Markups-1: Intro)

• Markups-2: Resampling Curves)

• Patch-based semiLM -includes transfer of semiLMs

• PseudoLMGenerator

• MarkupEditor

• MergeMarkups

• GPA-1: Setting the analysis

• GPA-2: Interactive 3D visualization of PCA space

Day 3: Friday April 30th

• ALPACA: Automated Landmarking through Point Cloud Alignment
• Putting everything together
• Landmarking decision tree
• Moving data into R (the new SlicerMorphR package).
• Auto3dGM
• Simulating deformations via Fiducial Registration Wizard
• Odds and ends, Q&A

Tutorials for Friday April 23rd

• ALPACA

• ALPACA video explanation by Dr. Porto

• Auto3Dgm)

• Auto3Dgm video tutorial

• Moving Data to R