Motion monitoring has shown helpful in MRI, particularly in long acquisitions such as 2D echo-planar imaging for fMRI. The most widely-used motion monitoring for fMRI relies on volume-to-volume registration (VVR). However, motion happens at the slice level, and VVR is insufficiently sensitive to intra-volume motion. In this work, we present the first slice-by-slice self-navigated motion monitoring system for MRI via a real-time slice-to-volume registration (SVR) algorithm. Extensive experiments demonstrated that our approach provides accurate motion measurements, and allows adaptive acquisition that ensures sufficient amount of data, while not acquiring data in excess, leading to improved data quality and reduced costs.