Background: 99m-Tc Ethyl-Cysteinate-Dimer SPECT and MR imaging play a significant role in diagnosing anosmia. In this study, two-tissue class and three-tissue class attenuation maps (2C-MR and 3C-MR) obtained from MR images were compared with CT-based attenuation correction (CTAC). Afterward, the presence of hypo-perfusion in brain lobes was evaluated in SPECT images. Materials and Methods: The 2C-MRAC map was generated through segmentation of T1-W MR images into air and soft-tissue, while in the 3C-MRAC map, the cortical bone was also considered. For investigating MRAC approaches, the difference between activity concentration (ACC) values was estimated in 144 volumes of interest. Ten normal and fourteen anosmic patients were compared by calculating the average normalized count and standard uptake value ratio parameters in the brain lobes. Results: The comparison between attenuation correction strategies represented that MRAC images resulted in underestimation of the ACC values which was more substantial in the cortical area rather than in central regions (maximum 9% vs. 6% for 2C-MR and maximum 5.5% vs. 3.5% for 3C-MR). Nevertheless, there was a strong correlation between the MRAC and CTAC methods with a correlation coefficient of 0.7 for both 2C-MR and 3C-MR. The statistical analysis between normal and affected groups indicated the hypo-perfusion in the cortex of Lh_frontal, Rh and Lh_temporal lobes with p-values < 0.05. Conclusions: Using MRAC resulted in underestimation of activity concentration which was partly eliminated by considering the cortical bone in the 3C-MR attenuation map. Hypo-perfusion was perceived in Frontal and Temporal lobes in SPECT-MRAC images of the anosmic group.