Functional magnetic resonance imaging (fMRI) in conscious animals is evolving as a critical tool for neuroscientists. The present study explored the effectiveness of an acclimation procedure in minimizing the stress experienced by the animal as assessed by alterations in physiological parameters including heart rate, respiratory rate, and serum corticosterone levels. Results confirm that as the stress of the protocol is minimized, there is a significant decrease in head movements and enhancement in data quality. The feasibility of improving the quality of fMRI data acquired in alert rats by utilizing a relatively simple technique is presented.