Segmentation recipes for 3D Slicer

Recipes for solving common image segmentation tasks using 3D Slicer.

• Skin surface extraction
• Craniotomy (splitting segments)
• Merge segments
• Aorta segmentation (fast, using Fast marching)
• Aorta segmentation (high-accuracy, using Grow from seeds)
• Cerebral vessel segmentation by subtraction
• Segmentation on arbitrarily oriented slices
• Skull stripping (keep brain region and remove skull bone and soft tissues) on CT

External links:

• Whole heart segmentation from CTA:
  • Video tutorial by Andras Lasso
  • Video tutorial by Justin Cramer
• Spine segmentation from CT:
  • Video tutorial and slides: Spine segmentation from CT and combining with 3D models
• Femur and pelvis segmentation from CT:
  • Video tutorial
• Segmentation video tutorials from CHU de Rouen (France): many step-by-step segmentation tutorials, including liver, wrist bones, lungs, kidneys, hip, and various animals.
• Kitware’s 3D Slicer segmentation tutorial slides

Obsolete recipes (we have better tools now)

• Skin surface extraction using region growing