jilei-hao / cmrep

Continuous Medial Representation

cmrep: Continuous Medial Representation

This software repository contains the source code for the cm-rep algorithms described in a series of papers by Yushkevich et al.

CM-Rep is a method for representing 3D biological objects (e.g, lungs, hippocampi) using a deformable model with predefined medial axis geometry. It allows the shape of these objects to be analyzed in terms of features derived from the medial axis, such as regional thickness. For more about the cm-rep methods, see these citations:

• Yushkevich, P.A., Zhang, H. and Gee, J.C., 2006. Continuous medial representation for anatomical structures. IEEE transactions on medical imaging, 25(12), pp.1547-1564. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4016176

• Yushkevich, P.A., 2009. Continuous medial representation of brain structures using the biharmonic PDE. NeuroImage, 45(1), pp.S99-S110. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680440/

• Yushkevich, P.A., Zhang, H., Simon, T.J. and Gee, J.C., 2008. Structure-specific statistical mapping of white matter tracts. NeuroImage, 41(2), pp.448-461. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519052/

• Pouch, A.M., Tian, S., Takebe, M., Yuan, J., Gorman, R., Cheung, A.T., Wang, H., Jackson, B.M., Gorman, J.H., Gorman, R.C. and Yushkevich, P.A., 2015. Medially constrained deformable modeling for segmentation of branching medial structures: Application to aortic valve segmentation and morphometry. Medical image analysis, 26(1), pp.217-231. http://www.sciencedirect.com/science/article/pii/S1361841515001401

Documentation:

• https://cmrep.readthedocs.io/