Previously we studied the effect of spatiotemporal pattern of transients on perceptual organization. Transient synchrony/asynchrony was critical in novel illusions of contextual motion (Likova & Tyler, 2002, 2003a, b). We found that strong image segmentation can be generated from transient asynchronies in fields of homogeneous visual noise, a phenomenon that we term 'Structure-from-Transients' (SfT). Here we used fMRI to reveal cortical mechanisms involved in SfT. The stimuli were random dot fields of 30 x 40°, replaced by uncorrelated dots every 500 ms. Asynchronous updates in subregions of the random-dot fields results in SfT. Exp.1: Figure/ground organization was generated in the test stimuli by transient-asynchrony between a figure area (a horizontal noise strip 8 x 40°) and its surround. The transient changes in the null stimuli however were synchronized, generating no SfT. Thus the global percepts switched from figure/ground (test) to a homogenous field (null) every 9 s, in 36 blocks per scan. Exp.2: Figure/ground organization was eliminated by segmentation of the field into equal horizontal SfT stripes. We found dramatic reorganization of the cortical activation pattern with manipulation of the perceptual SfT organization. Exp.1 revealed excitation of hMT/V5+ and figure/ground-specific top-down suppression of the background region in V1. Both were abolished by eliminating the figure/ground organization with multiple SfT stripes, which instead activated the higher dorsal and ventral tier retinotopic areas. The results support a view of a recurrent architecture with functional feedback loops, exhibiting complex spatiotemporal behavior in the case of a figure/ground organization extracted from its specific 'generator'. Our study reveals that on a global level the brain makes an important use of asynchrony as a relation structuring the spatiotemporal visual input.