The spinal cord is highly complex, consisting of a specialized neural network that comprised both neuronal and non-neuronal cells. Any kind of injury and/or insult to the spinal cord leads to a series of damaging events resulting in motor and/or sensory deficits below the level of injury. As a result, muscle paralysis (or paresis) leading to muscle atrophy or shrinking of the muscle along with changes in muscle fiber type, and contractile properties have been observed. Traditionally, histology had been used as a gold standard to characterize spinal cord injury (SCI)-induced adaptation in spinal cord and skeletal muscle. However, histology measurements is invasive and cannot be used for longitudinal analysis. Therefore, the use of conventional magnetic resonance imaging (MRI) is promoted to be used as an alternative non-invasive method, which allows the repeated measurements over time and secures the safety against radiation by using radiofrequency pulse. Currently, many of pathological changes and adaptations occurring after SCI can be measured by MRI methods, specifically 3-dimensional MRI with the advanced diffusion tensor imaging technique. Both techniques have shown to be sensitive in measuring morphological and structural changes in skeletal muscle and the spinal cord.