Setup and data analysis for functional magnetic resonance imaging of awake cat visual cortex

Functional magnetic resonance imaging (fMRI) is one of the most commonly used methods in cognitive neuroscience on humans. In recent decades, fMRI has also been used in the awake monkey experiments to localize functional brain areas and to compare the functional differences between human and monkey brains. Several procedures and paradigms have been developed to maintain proper head fixation and to perform motion control training. In this study, we extended the application of fMRI to awake cats without training, receiving a flickering checkerboard visual stimulus projected to a screen in front of them in a block-design paradigm. We found that body movement-induced non-rigid motion introduced artifacts into the functional scans, especially those around the eye and neck. To correct for these artifacts, we developed two methods: one for general experimental design, and the other for studies of whether a checkerboard task could be used as a localizer to optimize the motion-correction parameters. The results demonstrated that, with proper animal fixation and motion correction procedures, it is possible to perform fMRI experiments with untrained awake cats.