Monitoring cortical responses to neuromodulation on preclinical models can elucidate fundamental mechanisms of brain function. Concurrent brain stimulation and imaging is challenging, usually compromising spatiotemporal resolution, accuracy, and versatility. Here, we report on a non-invasive brain stimulation system with electronic control of neuromodulation parameters in a 9.4-T magnetic resonance imaging (MRI) environment. In the imaging scanner, multi-coil transcranial magnetic stimulation (mTMS) is delivered with a 2-coil array, and the MRI signal is measured with a radiofrequency coil. The mTMS can change the stimulus orientation with 1° resolution in a millisecond. Without physically rotating the coils, we evoked orientation-specific muscle responses after cortical stimulation on an anesthetized rat. The mTMS system was successfully implemented and tested with the small-animal MRI, showing minimal interference with B 0 and B 1 + fields and uncompromised image quality. A delay of 40 ms between the stimulation pulse and fMRI acquisition—similar or even shorter than those previously described in humans—led to artifact-free images. Concurrent electronically targeted brain stimulation and neuroimaging provides a valuable tool for exploring whole-brain network functions, endorsing more efficient treatment protocols.

Functional MRI (fMRI) is a flexible tool for sensory perception studies in animal models. However, animal fMRI studies are generally performed under anesthesia. Unfortunately, anesthesia affects brain function and sensory processing, complicating the interpretation of the findings. Since there is a growing need for fMRI protocols applicable for awake animals, we optimized a zero echo time Multi-Band Sweep Imaging with a Fourier Transformation (MB-SWIFT) fMRI approach for imaging awake mice. We implemented a 14-day habituation protocol that resulted in merely moderate motion of the mice while being head-fixed with the animals’ body and limbs being free to move. The sensory responsiveness between different states of consciousness was compared by imaging mice with visual and auditory stimulation schemes in the awake state and under ketamine–xylazine anesthesia. In awake mice, we observed a robust whole-brain activation of the ascending auditory and visual pathways, as well as higher sensory processing areas. Under ketamine–xylazine anesthesia, auditory responses were suppressed, and the temporal shapes of fMRI responses were different from those obtained in awake mice. Our results suggest that the quiet and motion-tolerant zero echo time MB-SWIFT approach allows complex behavioral fMRI designs in the awake state that promise to improve our understanding of the underlying mechanisms of perception.