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Structure Model Index

The structure model index (SMI) is a method for determining the plate- or rod-like geometry of trabecular structures. It uses the change in surface area (BS, from Isosurface) as volume increases infinitesimally to calculate SMI = 0 for plates, 3 for rods and 4 for solid spheres. Unfortunately SMI is negative in the case of concave surfaces, which are common in trabecular bone, making results difficult to interpret. Structure Model Index is included in BoneJ because the bone research community frequently uses SMI and because of the current lack of a better method for quantifying rodness and plateness. Two methods are implemented; one uses surface mesh dilation and is preferred, whereas the other uses voxel dilation (Dilate 3D) and is only implemented because that is how the SkyScan™ technical manual describes the algorithm in CTAn (it doesn't work very convincingly in our hands).

Hildebrand T, Rüegsegger P (1997) Quantification of bone microarchitecture with the structure model index. Comput. Methods Biomech. Biomed. Engin. 1: 15-23. doi:10.1080/01495739708936692.

Structural parameters measured by the SkyScan™ CT-Analyser software. SkyScan AB. http://www.skyscan.be/next/CTAn03.pdf

• Input
  • Binary stack
• Options
  • SMI Method:
    • Hildebrand & Rüegsegger: Surface mesh dilation, preferred
    • SkyScan: Voxel dilation, for method comparison only
  • Voxel resampling: How much to resample voxels during mesh creation; a higher number gives a smoother mesh and faster processing but misses fine detail
  • Mesh Smoothing: How much to smooth the mesh after it has been created. Seems not to have a substantial effect on SMI
• Output
  • Image: Image title
  • SMI: Structure model index: plate = 0; rod = 3; sphere = 4; concave < 0.
  • Verbose logging:
    • Fraction of surface area that is concave: calculated from the sum of the areas of triangles in the surface mesh that get smaller when the volume is dilated
    • Convex SMI: SMI calculated from the change in area of the triangles that enlarge during volume dilation
    • Concave SMI: SMI calculated from the change in area of the triangles that shrink during volume dilation

This file last modified 0803hrs 28 July 2011 © Michael Doube 2004-2012 :: Designed to be interoperable and standards-compliant.