BACKGROUND: Several networks of synchronous blood oxygen level dependent (BOLD) oscillations have been identified in the brain during the resting state. The aim of this study was to further characterize the dynamic nature of the brain at rest by investigating the presence and distribution of coherent, transient BOLD activity in resting fMRI data using a novel method of fMRI data analysis--2dTCA. MATERIAL/METHODS: High-field fMRI data were acquired in 27 subjects. The temporal clustering analysis, 2dTCA, was implemented to determine the timing of significant, spatially coherent, transient BOLD signal changes. Group maps of positive and negative coherent BOLD changes from each timing profile were created. RESULTS: Spontaneous increases in BOLD activity at both 3T and 4T and decreases at 4T were found in regions of the alpha rhythm circuit including the thalamus, precuneus and the occipital cortex. Additional positive and negative oscillations at 4T and a small region of positive activity at 3T were identified in the area of the brain stem reticular formation, the control center for maintaining arousal and motivation. CONCLUSIONS: These results provide additional evidence for the presence of dynamic functional networks in the resting brain that are active while the subjects appear to be at rest and that are spatially distributed in areas responsible for maintaining consciousness and vigilance including brain stem. These findings should be considered in interpreting fMRI results which use resting baseline for comparisons.