Ectopic adiposity has gained considerable attention because of its tight association with metabolic and cardiovascular health in persons with spinal cord injury (SCI). Ectopic adiposity is characterized by the storage of adipose tissue in non-subcutaneous sites. Magnetic resonance imaging (MRI) has proven to be an effective tool in quantifying ectopic adiposity and provides the opportunity to measure different adipose depots including intermuscular adipose tissue (IMAT) and intramuscular adipose tissue (IntraMAT) or in-tramuscular fat (IMF). It is highly important to distinguish and clearly define these compartments, because controversy still exists on how to accurately quantify these adipose depots. Investigators have relied on separating muscle from fat pixels based on their characteristic signal intensities. A common technique is plotting a threshold histogram that clearly separates between muscle and fat peaks. The cut-offs to separate between muscle and fat peaks are still not clearly defined and different cut-offs have been identified. This review will outline and compare the Midpoint and Otsu techniques, two methods used to determine the threshold between muscle and fat pixels on T1 weighted MRI. The process of water/fat segmentation using the Dixon method will also be outlined. We are hopeful that this review will trigger more research towards accurately quantifying ectopic adiposity due to its high relevance to cardiometabolic health after SCI.