Tomographic image reconstruction requires precise geometric measurements and calibration for the scanning system to yield optimal images. The isocenter offset is a very important geometric parameter that directly governs the spatial resolution of reconstructed images. Due to system imperfections such as mechanical misalignment, an accurate isocenter offset is difficult to achieve. Common calibration procedures used during isocenter offset tuning, such as pin scan, are not able to reach precision of subpixel level and are also inevitably hampered by system imperfections. We propose a purely data-driven method based on Fourier shift theorem to indirectly, yet precisely, estimate the isocenter offset at the subpixel level. The solution is obtained by applying a generalized M-estimator, a robust regression algorithm, to an arbitrary sinogram of axial scanning geometry. Numerical experiments are conducted on both simulated phantom data and actual data using a tungsten wire. Simulation results reveal that the proposed method achieves great accuracy on estimating and tuning the isocenter offset, which, in turn, significantly improves the quality of final images, particularly in spatial resolution.