Recent electrophysiological studies have reported short latency modulations in cortical regions for multisensory stimuli, thereby suggesting a subcortical, possibly thalamic origin of these modulations. Concurrently, there is an ongoing debate, whether multisensory interplay reflects automatic, bottom-up driven processes or relies on top-down influences. Here, we dissociated the effects of task set and stimulus configurations on BOLD-signals in the human thalamus with event-related functional magnetic resonance imaging (fMRI). We orthogonally manipulated temporal and spatial congruency of audio-visual stimulus configurations, while subjects judged either their temporal or spatial congruency. Voxel-based fMRI results revealed increased fMRI-signals for the temporal versus spatial task in posterior and central thalamus, respectively. A more sensitive region of interest (ROI)-analysis confirmed that the posterior thalamic nuclei showed a preference for the temporal task and central thalamic nuclei for the spatial task. Moreover, the ROI-analysis also revealed enhanced fMRI-signals for spatially incongruent stimuli in the central thalamus. Together, our results demonstrate that both audio-visual stimulus configurations and task-related processing of spatial or temporal stimulus features selectively modulate thalamic processing and thus are in a position to influence cortical processing at an early stage.

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