The spinal cord (SC) is the caudal extension of the Central Nervous System (CNS) and is responsible for several complex functions. Among imaging methods, functional Magnetic Resonance Imaging (fMRI) represents the most promising tool for non-invasive investigation of SC functions/dysfunctions. However, the utilization of SC-fMRI is widely under-exploited, either due to challenges in acquiring good quality data, or to the lack of dedicated analysis tools. In this study, we implemented an optimized experimental approach and defined a pipeline for SC-fMRI data analysis. We validate such pipeline and investigate the impact of acquisition direction on noise removal.