Degeneration of intervertebral discs can lead to various health problems, among which low back pain is the most common. Studies concerning methods of dealing with that problem are being conducted and magnetic resonance imaging is one of the most popular methods of assessing their progress. Many of these studies are based on animal models. The paper links these two facts and so it contains the description of methodology that can be used for assessing the degree of degeneration of the porcine intervertebral discs based on scans obtained in MRI study. Proposed method uses Otsu method of automatic thresholding and next basic operators of morphological image processing. The outcome is binary mask giving direct information about locations of intervertebral discs in MRI scans. The obtained mask can be also used to separate locations of intervertebral discs in following MRI studies of the same animals, in cases where they are much harder to delineate due to their degeneration. The paper shows also exemplary results demonstrating usefulness of proposed methodology for the evaluation of discs treatment using mesenchymal stem cells.