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Background Glaucoma is a neurodegenerative disease that affects both the retina and central visual pathway. Magnetization transfer imaging (MTI) is a sensitive magnetic resonance imaging (MRI) technique that can detect degenerative changes in the brain. Purpose To investigate the geniculocalcarine (GCT) and striate areas in primary glaucoma patients using region of interest (ROI) analysis of magnetization transfer ratio (MTR). Material and Methods Twenty patients with primary glaucoma in both eyes were compared with 31 healthy control patients. All of the participants were examined on a 3.0 T scanner using a three-dimensional T1-weighted spoiled gradient recalled acquisition (SPGR) with and without a MT saturation pulse. A two-sample t-test was used to evaluate the MTR difference between the groups. P < 0.05 was used to determine statistical significance. Results The MTR of the glaucoma group was lower than the healthy controls in both the bilateral GCT (t = 3.781, P = 0.001) and striate areas (t = 4.177, P = 0.000). Conclusion The MTR reductions in the bilateral GCT and striate areas suggest that there is GCT demyelination and striate area degeneration in primary glaucoma. These neurodegenerative effects may be induced as a direct effect of retrograde axonal degeneration along with the indirect effect of anterograde trans-synaptic degeneration.