Functional MRI of the Brainstem: Common Problems and their Solutions

Functional magnetic resonance imaging (fMRI) of the brainstem is a relatively young field that is rapidly evolving. While it is still difficult to obtain usable fMRI signals from this complicated brain region, the past few years have seen a number of important advances that bring us closer to routine application of this method in the clinical and scientific setting. This review gives an overview of the technical capabilities and limitations of brainstem fMRI. It explains the major brainstem-specific problems and gives advice on how to avoid or counteract them. In particular, I discuss how spatial resolution issues can be overcome by using appropriate sequences, coils, and spatial preprocessing, how the effects of physiological noise can be mitigated by noise modeling and spatial masking, and how the functional heterogeneity of brainstem nuclei needs to be taken into account, when planning a study. Solving these common problems is a prerequisite for any scientist or clinician interested in applying fMRI to measure brainstem activity.