<h3>Background</h3> Inflammation of the temporomandibular joint (TMJ) has a relatively high correlation (> 17%) to the late stages of rheumatoid arthritis (RA). RA is a chronic inflammatory autoimmune disease that causes cartilage and bone destruction. Cell activity of TMJ was measured by using 2 radiotracers, [18 F]-fluoro-2-deoxy-D-glucose (FDG) and [18 F]-sodium fluoride (NaF), for staging and surveillance of RA. <h3>Objective</h3> The aim of this study was to quantify the region of interest (ROI) volumes of FDG- and NaF-based TMJ positron emission tomography (PET) images by using the ROVER software. <h3>Materials and Methods</h3> Institutional review board (IRB) approval was obtained for 20 previously diagnosed patients with RA. From this cohort, 17 anonymized patients with NaF and FDG-PET/CT scans were reviewed by 3 calibrated investigators. When there was disagreement, a fourth investigator who is an expert in PET/CT, was used. The standardized uptake values corrected (SUV-Mean Cor) were calculated and recorded on ROVER. The collected data and literature review findings were collated and analyzed to provide a holistic comparison table. The clinical applications, advantages, and disadvantages of 8 imaging techniques were reviewed. <h3>Results</h3> The average ROI volumes differed between FDG- and NaF-based PET images in every case, showing a higher quantification for NaF-based scans. In 1 case, ROI mean total corrected value was 23.25 when NaF-PET was used, as opposed to 6.7 when FDG-PET was used. There was a similar trend among other cases included in the study. The NaF-PET ROI values appeared higher than the standard FDG-PET ROI values in the cases where the RA activity was quantified. SUV can be obtained by dividing the ROI activity concentration (KBq/L) by the decay-corrected amount of injected FDG (KBq/L) times the weight of the patient in grams. ROVER automatically calculates the average and maximum SUVs for all patients. <h3>Discussion</h3> With the use of ROVER, it is possible to collect accurate measurements of TMJ disease activity from both FDG-PET and NaF-PET images. NaF-PET appeared to be a more sensitive technique.