Non-rigid image registration: Medical Image Registration Toolbox (MIRT)

MIRT project page and code. A Matlab toolbox for non-rigid image registration. It implements the Residual Complexity (RC) similarity measure as well as some other popular similarity measures. It supports parametric and non-parametric transformation estimation.

Point set registration:

Coherent Point Drift (CPD) algorithm project page and code. A matlab toolbox for point set registration, matching and correspondence recovering. It allows rigid, affine and non-rigid point-set registration. Supports 2D, 3D and higher dimensional (N-D) registration.

Some Matlab functions: Fast linear image interpolation, implemented as Matlab mex functions in C++. a) Use mirt2D_mexinterp to interpolate a single or a pile of 2D images fast and b) mirt3D_mexinterp to interpolate a single or a pile of 3D images fast.

mirt_dctn.m Multidimensional (N-D) discrete cosine transform (DCT).
mirt_idctn.m Multidimensional (N-D) inverse discrete cosine transform (IDCT).
The functions work significantly faster than Matlab's native dct, idct, dct2, idct2, and also allows N-D (3D, 4D, 5D, etc.) input.