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For individuals with spinal cord injuries, functional neuromuscular stimulation (FNS) systems can be used to activate paralyzed muscles in order to restore function, provide exercise, or assist in movement therapy. In previous work, the pattern generator/pattern shaper (PG/PS) adaptive controller was evaluated on subjects with spinal cord injuries and was able to automatically adjust stimulation parameters to account for individual subject differences and system response nonlinearities. In this study, the PG/PS control system was utilized in extended trials. Results indicated that the controller adapted stimulation patterns in an online manner to account for changes in system properties due to fatigue.