The primary objective of this study was to test quantification protocols on human abdominal and organ fat data acquired using magnetic resonance (MR) imaging or spectroscopy. Liver, pancreatic, visceral and subcutaneous fat in 10 obese patients with prediabetes were measured before and after a 12-week intermittent fasting programme with daily probiotic or placebo supplementation. All participants were scanned by a Siemens 3.0T MR scanner. The quantification of fat contents was performed using ImageJ (for MRI data) and SIVIC software (for MRS data). Two methods of quantifying pancreas fat were compared.