A new method for the numerical computation of the lifetimes of magnetic states within harmonic transition state theory (HTST) has been developed. In the simplest case, the system is described by a Heisenberg-like Hamiltonian with short-range interaction. Calculations are performed in Cartesian coordinates. Constraints on the values of magnetic moments are taken into account using Lagrange multipliers. The pre-exponential factor in the Arrhenius law in HTST is written in terms of the determinants of the Hessian of energy at the minima and saddle points on the multidimensional energy surface. An algorithm for calculating these determinants without searching for eigenvalues of the Hessian but using recursive relations is proposed. The method allows calculating determinants for systems containing millions of magnetic moments. This makes it possible to calculate the pre-exponential factor and estimate the lifetimes of micron-scale topological structures with atomic resolution, which until now has been impossible using standard approaches. The accuracy of the method is demonstrated by calculating 2D and 3D skyrmionic structures.