Background: Polymer gel dosimeters combined with magnetic resonance imaging (MRI) can be used for dose verification of advanced radiation therapy techniques. However, the uncertainty of dose map measured by gel dosimeter should be known. The purpose of this study is to investigate the uncertainty related to calibration curve and MRI protocol for MAGIC (Methacrylic and Ascorbic acid in Gelatin Initiated by Copper) gel and finally ways of optimization MRI protocol is introduced.Materials and Methods: MAGIC gel was prepared by the Fong et al. instruction. The gels were poured into calibration vials and irradiated by 18 MV photons. 1.5 Tesla MRI was used for reading out information. Finally, uncertainty of measured dose was calculated.Results: Results show that for MAGIC polymer gel dosimeter, at low doses, the estimated uncertainty is high (≈ 18.96% for 1 Gy) but it reduces to approximately 4.17% for 10 Gy. Also, with increasing dose, the uncertainty for the measured dose decreases non-linearly. For low doses, the most significant uncertainties are σR0 (uncertainty of intercept) and σa (uncertainty of slope) for high doses. MRI protocol parameters influence signal-to-noise ratio (SNR).Conclusion: The most important source of uncertainty is uncertainty of R2. Hence, MRI protocol and parameters therein should be optimized. At low doses, the estimated uncertainty is high and reduces by increasing dose. It is suggested that in relative dosimetry, gels are irradiated by high doses in linear range of given gel dosimeter and then scaled down to the desired dose range.