When observing bistable stimuli, the percept can change in the absence of changes in the stimulus itself. When intermittently presenting a bistable stimulus, the number of perceptual alternations can increase or decrease, depending on the duration of the period that the stimulus is removed from screen between stimulus presentations (off-period). Longer off-periods lead to stabilization of the percept, while short off-periods produce perceptual alternations. Here we compare fMRI brain activation across percept repetitions and alternations when observing an intermittently presented ambiguously rotating structure from motion sphere. In the first experimental session, subjects were requested to voluntarily control the percept into either a repeating or an alternating perceptual regime at a single off-period. In a consecutive session, subjects observed the sphere uninstructed, and reported alternations and repetitions. The behavioral data showed that there were marked individual biases for observing the sphere as either repeating or alternating. The fMRI data showed activation differences between alternating and repeating perceptual regimes in an extensive network that included parietal cortex, dorsal premotor area, dorsolateral prefrontal cortex, supplementary motor area, insula, and cerebellum. However, these activation differences could all be explained by intersubject differences in the bias for one of the two perceptual regimes. The stronger the bias was for a particular perceptual regime, the less activation and vice versa. We conclude that widespread activation differences between perceptual regimes can be accounted for by differences in the perceptual bias for one of the two regimes.