Due to the nonlinear deformation of nonrigid and nonuniform tissues, it is challenging to accurately measure the displacements of feature points distributed on the inner parts, boundaries, and separatrices of tissue layers. To address this challenge, we propose a feature point matching technique called RAPID to measure MR 2D slice deformation of nonuniform and nonrigid biological tissues. We propose to use the covariance of several neighboring point statistics computed around a keypoint, as the keypoint descriptor. Inspired by the kernel methods, we advocate adopting a Riemannian pseudo kernel to map SPD matrices to a high dimensional Hilbert space, where the Euclidean geometry applies. We compare our RAPID with two existing schemes (i.e., SIFT and SURF). Our experimental results show that our RAPID is superior to SIFT and SURF, because the benefits offered by RAPID are two-fold. First, our RAPID increases the number of matched data points. Second, RAPID substantially improves the key-point matching accuracy of SIFT and SURF.