Only listing software that are actively used and maintained.

The package computes the Wasserstein distance of persistent diagrms on graph filtations. Then show how to perform topological inference and unsupervised learning. https://pages.stat.wisc.edu/~mchung/dynamicTDA/

The packge performs the online version of the permutation test called the transpostion test. Various inference settings are illustrated. https://pages.stat.wisc.edu/~mchung/transpositions/

The package performs the exact topolgical inference on Betti-0 and Betti-1 curves obtained in graph data structures. The method can be used to topologically quantify the brain network differences. https://pages.stat.wisc.edu/~mchung/TDA/

The package performs heat kernel smoothing on surface mesh data including brain surfaces. The method will increase the singal-to-noise ratio and statistical power of surface data https://pages.stat.wisc.edu/~mchung/softwares/hk/hk.html

The packge peforms the weighted version of spherical harmonic (SPHARM) represetnation of surface meshes including brain surfaces. https://pages.stat.wisc.edu/~mchung/softwares/weighted-SPHARM/weighted-SPHARM.html

The package performs the finite element method (FEM) based estimation of the eigenfunctions of the Laplace-Beltrami (LB) operator on surface meshes. Then use it to perform Fourier expansion on brain surfaces. http://brainimaging.waisman.wisc.edu/%7Echung/lb/

The package extnds the functionality of SurfStat in modeling amygdala surface mesh data. It includes the diffusion based amygdala surface matching. https://pages.stat.wisc.edu/~mchung/research/amygdala/

The package perfoms the cosine series reprentation of functional data and curves including white matter fiber traccts. http://brainimaging.waisman.wisc.edu/%7Echung/tracts/

The package distributes the brain structural covarite network data published in Chung, M.K., Hanson, J.L., Ye, J., Davidson, R.J. Pollak, S.D. 2015 Persistent homology in sparse regression and its application to brain morphometry. IEEE Transactions on Medical Imaging, 34:1928-1939. The package shows how to compute Betti-0 curve over graph filtrations. http://brainimaging.waisman.wisc.edu/%7Echung/barcodes/

The package distribtues the Amygdala/hippocampus surface mesh data and mesh procesing pipeline. https://brainimaging.waisman.wisc.edu/%7Echung/midus/

The package performs the mandible shape analysis and performs the random field theory based statistical inference. https://pages.stat.wisc.edu/~mchung/mandible/

The package build dense structural brain networks without parcellatio. http://brainimaging.waisman.wisc.edu/%7Echung/graph/

The package performs the Morse filtraions for 1D/2D functional data and produces corresponding persistent diagrams. http://brainimaging.waisman.wisc.edu/~chung/persistence/