- 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.
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
- 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