Evoked fMRI findings of anesthetized mice are inconsistent possibly due to uncontrolled vascular physiology. In our studies under ketamine and xylazine anesthesia, localized BOLD response was observed in the spontaneously breathing condition, which is known to cause hypercapnia. Here we performed blood gas analysis and functional studies of spontaneously breathing vs. mechanical ventilating mice. The mechanical ventilation maintained mice at normal physiology and induced larger hemodynamic and BOLD responses to forepaw stimulation. Spontaneous breathing induced severe hypercapnia and acidosis, but surprisingly showed significant evoked functional responses. These results suggest that both methods can be used for functional experiments.