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Summary: The hierarchical organization of the visual system preserves topology, which is often lost in the “raw” human retinotopic maps derived from BOLD fMRI recordings. Here, we present the protocol for generating topology-preserving and smooth retinotopic maps from human retinotopy fMRI data. We describe data pre-processing, 3D surface flattening, and selection of the region of interest (ROI), followed by smoothing of the retinotopic maps within the ROI. This approach can be applied to visual cortical areas V1, V2, and V3 simultaneously.For complete details on the use and execution of this protocol, please refer to Tu et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.