Purpose <p>The aim was to establish a functional MRI protocol for analyzing human stereoscopic vision in clinical practice. The feasibility was established in a cohort of 9 healthy subjects to determine the functional cortical areas responsible for virtually relief vision.</p> Methods <p>Nine healthy right-handed subjects underwent orthoptic examination and functional MRI. The activation paradigms used were based on a block sequence with the projection of static and dynamic 2D and 3D test patterns during three experiments. The test patterns were projected through two separate eyepieces to create stereoscopic vision. SPM software was used for post-processing and data analysis.</p> Results <p>Among the three different test patterns used, the second, which corresponded to a static high-relief image of a billiard, appeared to be significant for identifying cortical area activation during stereoscopy. In the group analysis, only areas V3A and V6 showed statistically significant activation. Individual analysis revealed activation of the rostral IPS and V5/MT+.</p> Conclusion <p>More data is needed to determine the precise cortical area of activation for stereoscopy. This study proposes a useful and accessible method for functional MRI analysis of stereoscopy.</p>