The spinal cord plays a central role in regulating sensorimotor functions through complex neural pathways. However, detailed investigation of these mechanisms remains a developing field. In this study, we propose a multimodal approach combining transcranial magnetic stimulation (TMS) for reliable motor cortex stimulation with functional magnetic resonance imaging (fMRI) of spinal cord. In a cohort of twelve participants, we assessed blood oxygenation level dependent (BOLD) signal changes in the cervical spinal cord across three TMS-intensity conditions (low, medium, and high, relative to the individual's resting motor threshold). Given challenges with SNR for spinal cord fMRI, we propose to apply the sparsity-pursuing deconvolution framework known as total activation (TA). The TA framework significantly improves retrieval of task-related activity as assessed by the statistical significance of the regression model expressed in the deconvolved domain, as well as the interpretation of the activation patterns. Our findings demonstrate that transcranial stimulation can modulate spinal cord activity in a stimulus-dependent manner, disentangling the underlying sensory and motor neuron populations. These results highlight the potential of a novel multimodal approach to reliably image and modulate spinal cord activity via cortical TMS when proper attention is given to the signal processing steps.