@article{9a4674dee2544e0d952d819195da0e2f,
title = "Protocol for topology-preserving smoothing of BOLD fMRI retinotopic maps of the human visual cortex",
abstract = "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).",
keywords = "Cognitive neuroscience, Computer sciences, Neuroscience",
author = "Yanshuai Tu and Xin Li and Lu, {Zhong Lin} and Yalin Wang",
note = "Funding Information: Y.T. Z.L. and Y.W. were partially supported by the Directorate for Mathematical and Physical Sciences of the National Science Foundation, grant no. 1413417 to D.T. Y.T. and Y.W. and grant no. 1412722 to Z.L. Y.T. X.L. Z.L. and Y.W. were partially supported by National Eye Institute, grant no. R01EY032125. Y.T. and Y.W. were partially supported by the National Institute on Aging, grant no. R21AG065942; the National Institute of Biomedical Imaging and Bioengineering, grant no. R01EB025032; National Institute of Dental & Craniofacial Research, grant no. R01DE030286; and Arizona Alzheimer's Consortium. The funders had no role in the study design, data collection, and analysis, decision to publish, or preparation of the manuscript. Y.T.: methodology, conceptualization, software, original draft preparation. X.L.: software organization and management, manuscript draft. Z.L.L.: methodology, supervision, review and editing, funding. Y.W.: methodology, supervision, review and editing, project administration, funding. Y.T. Z.L. and Y.W. have a joint patent application: Tu, Y. Y. Wang, and Z.-L. Lu, Methods and Systems for Precise Quantification of Human Sensory Cortical Areas, U.S. Patent Application No. 63/004. 2020. Funding Information: Y.T., Z.L., and Y.W. were partially supported by the Directorate for Mathematical and Physical Sciences of the National Science Foundation , grant no. 1413417 to D.T., Y.T., and Y.W., and grant no. 1412722 to Z.L. Y.T., X.L., Z.L., and Y.W. were partially supported by National Eye Institute , grant no. R01EY032125 . Y.T. and Y.W. were partially supported by the National Institute on Aging , grant no. R21AG065942 ; the National Institute of Biomedical Imaging and Bioengineering , grant no. R01EB025032 ; National Institute of Dental & Craniofacial Research , grant no. R01DE030286 ; and Arizona Alzheimer{\textquoteright}s Consortium. The funders had no role in the study design, data collection, and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2022 The Author(s)",
year = "2022",
month = sep,
day = "16",
doi = "10.1016/j.xpro.2022.101614",
language = "English (US)",
volume = "3",
journal = "STAR Protocols",
issn = "2666-1667",
publisher = "Cell Press",
number = "3",
}