{ "_id": "6a2075a6cd65a98ecbd13155", "Package": "neurosurf", "Type": "Package", "Title": "Data Structures and Visualization for Surface-Based Neuroimaging\nData", "Version": "0.1.0", "Authors@R": "c(\nperson(c(\"Bradley\", \"R\"), \"Buchsbaum\", role = c(\"aut\", \"cre\", \"cph\"), email = \"brad.buchsbaum@gmail.com\"))", "Description": "A comprehensive toolkit for working with surface-based\nneuroimaging data represented as triangle meshes. The package\nprovides classes and methods for creating, manipulating, and\nvisualizing 3D surface geometries (e.g., cortical surfaces),\nwith support for various file formats including FreeSurfer and\nGIFTI. Key features include: surface smoothing, curvature\ncomputation, neighborhood graph construction, geodesic distance\ncalculations, searchlight analysis for surface-based machine\nlearning, and interactive 3D visualization via HTMLWidgets. 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NeuroSurfaceVector Objects", "topics": [ "Arith,NeuroSurfaceVector,NeuroSurface-method", "Arith,NeuroSurfaceVector,NeuroSurfaceVector-method", "Arith,NeuroSurfaceVector,numeric-method", "Arith,numeric,NeuroSurfaceVector-method" ] }, { "page": "as-methods", "title": "Coercion Methods for NeuroSurface Objects", "topics": [ "as" ] }, { "page": "as.matrix-methods", "title": "Convert Surface Data to Matrix", "topics": [ "as.matrix,BilatNeuroSurfaceVector-method", "as.matrix,NeuroSurfaceVector-method", "as.matrix,ROISurfaceVector-method" ] }, { "page": "as.vector-methods", "title": "Convert Surface Data to Vector", "topics": [ "as.vector,NeuroSurface-method" ] }, { "page": "BilatNeuroSurfaceVector-class", "title": "Bilateral NeuroSurface Vector Class", "topics": [ "BilatNeuroSurfaceVector-class" ] }, { "page": "clear_geodesic_cache", "title": "Clear geodesic cache", "topics": [ "clear_geodesic_cache" ] }, { "page": "cluster_threshold-methods", "title": "Apply Cluster-Extent Threshold to Surface Data", "topics": [ "cluster_threshold", "cluster_threshold,NeuroSurface-method", "cluster_threshold,NeuroSurfaceVector-method" ] }, { "page": "ColorMappedNeuroSurface", "title": "ColorMappedNeuroSurface", "topics": [ "ColorMappedNeuroSurface" ] }, { "page": "ColorMappedNeuroSurface-class", "title": "ColorMappedNeuroSurface", "topics": [ "ColorMappedNeuroSurface-class" ] }, { "page": "Compare-NeuroSurface-method", "title": "Comparison Operations for NeuroSurface Objects", "topics": [ "Compare,NeuroSurface,NeuroSurface-method" ] }, { "page": "Compare-NeuroSurface-numeric-method", "title": "Comparison Operations for NeuroSurface Objects", "topics": [ "Compare,NeuroSurface,numeric-method" ] }, { "page": "Compare-NeuroSurfaceVector-method", "title": "Comparison Operations for NeuroSurfaceVector Objects", "topics": [ "Compare,NeuroSurfaceVector,NeuroSurfaceVector-method", "Compare,NeuroSurfaceVector,numeric-method", "Compare,numeric,NeuroSurfaceVector-method" ] }, { "page": "compute_hull_world_cpp", "title": "Compute boundary hull points in world space (C++)", "topics": [ "compute_hull_world_cpp" ] }, { "page": "conn_comp-methods", "title": "Compute Connected Components on a Surface", "topics": [ "conn_comp,NeuroSurface-method", "conn_comp,NeuroSurfaceVector-method" ] }, { "page": "coords-methods", "title": "Extract Vertex Coordinates", "topics": [ "coords,igraph-method", "coords,NeuroSurface-method", "coords,NeuroSurfaceVector-method", "coords,ROISurface-method", "coords,SurfaceGeometry-method" ] }, { "page": "curv_cols", "title": "Convert Curvature Values to Binary Colors for Visualization", "topics": [ "curv_cols" ] }, { "page": "curv_cols_smooth", "title": "Convert Curvature Values to Smooth Gradient Colors", "topics": [ "curv_cols_smooth" ] }, { "page": "curvature-methods", "title": "Compute Surface Curvature Vector", "topics": [ "curv", "curvature", "curvature,SurfaceGeometry-method" ] }, { "page": "data_reader-methods", "title": "Create a Column Reader for Surface Data", "topics": [ "data_reader,NIMLSurfaceDataMetaInfo-method", "data_reader,SurfaceGeometryMetaInfo-method" ] }, { "page": "debug_surfwidget", "title": "Debugging Helper for surfwidget", "topics": [ "debug_surfwidget" ] }, { "page": "draw_surface_plot", "title": "Draw a static multi-panel surface figure", "topics": [ "draw_surface_plot" ] }, { "page": "faces-methods", "title": "Extract Faces from a Surface Object", "topics": [ "faces", "faces,NeuroSurface-method", "faces,NeuroSurfaceVector-method", "faces,SurfaceGeometry-method" ] }, { "page": "find_all_neighbors", "title": "Find Node Neighbors in a Surface Mesh", "topics": [ "find_all_neighbors" ] }, { "page": "find_nearest_vertex", "title": "Find the nearest surface vertex to a 3D point", "topics": [ "find_nearest_vertex" ] }, { "page": "find_roi_boundaries", "title": "Find boundaries of ROIs on a surface mesh", "topics": [ "find_roi_boundaries" ] }, { "page": "findBoundaries-methods", "title": "Find Boundaries Between Regions on a Surface", "topics": [ "findBoundaries", "findBoundaries,NeuroSurface-method" ] }, { "page": "FreesurferAsciiSurfaceFileDescriptor-class", "title": "FresurferAsciiSurfaceFileDescriptor", "topics": [ "FreesurferAsciiSurfaceFileDescriptor-class" ] }, { "page": "FreesurferBinarySurfaceFileDescriptor-class", "title": "FresurferBinarySurfaceFileDescriptor", "topics": [ "FreesurferBinarySurfaceFileDescriptor-class" ] }, { "page": "FreeSurferSurfaceGeometryMetaInfo-class", "title": "FreesurferSurfaceGeometryMetaInfo Class", "topics": [ "FreesurferSurfaceGeometryMetaInfo-class" ] }, { "page": "gaussian_splat", "title": "Gaussian splats on surface meshes", "topics": [ "gaussian_splat", "gaussian_splat_multi", "gaussian_splat_vertex" ] }, { "page": "geodesic_distance_matrix", "title": "All-pairs geodesic distance matrix (chunked)", "topics": [ "geodesic_distance_matrix" ] }, { "page": "geodesic_distances", "title": "Geodesic distances from sources to targets", "topics": [ "geodesic_distances" ] }, { "page": "geometry-methods", "title": "Extract Geometry from Surface Object", "topics": [ "geometry", "geometry,NeuroSurface-method", "geometry,NeuroSurfaceVector-method" ] }, { "page": "get_surface", "title": "Retrieve a geometry from a SurfaceSet", "topics": [ "get_surface" ] }, { "page": "GIFTISurfaceDataMetaInfo-class", "title": "GIFTISurfaceDataMetaInfo", "topics": [ "GIFTISurfaceDataMetaInfo-class" ] }, { "page": "GIFTISurfaceFileDescriptor-class", "title": "GIFTISurfaceFileDescriptor", "topics": [ "GIFTISurfaceFileDescriptor-class" ] }, { "page": "GIFTISurfaceGeometryMetaInfo-class", "title": "GIFTISurfaceGeometryMetaInfo", "topics": [ "GIFTISurfaceGeometryMetaInfo-class" ] }, { "page": "graph-methods", "title": "extract 'igraph' object", "topics": [ "graph", "graph,NeuroSurface-method", "graph,NeuroSurfaceVector-method", "graph,SurfaceGeometry-method" ] }, { "page": "indices-methods", "title": "Extract Vertex Indices", "topics": [ "indices,NeuroSurface-method", "indices,NeuroSurfaceVector-method", "indices,ROISurface-method", "indices,ROISurfaceVector-method" ] }, { "page": "LabeledNeuroSurface-class", "title": "LabeledNeuroSurface Class", "topics": [ "LabeledNeuroSurface-class" ] }, { "page": "laplacian-methods", "title": "Compute Graph Laplacian", "topics": [ "laplacian", "laplacian,SurfaceGeometry,missing,missing-method", "laplacian,SurfaceGeometry,missing,numeric-method" ] }, { "page": "left-methods", "title": "Get Left Hemisphere", "topics": [ "left", "left,BilatNeuroSurfaceVector-method" ] }, { "page": "length-methods", "title": "Get Length of Surface Object", "topics": [ "length,ROISurface-method" ] }, { "page": "load_data-methods", "title": "load_data", "topics": [ "load_data,FreesurferSurfaceGeometryMetaInfo-method", "load_data,GIFTISurfaceGeometryMetaInfo-method", "load_data,NeuroSurfaceSource-method", "load_data,NeuroSurfaceVectorSource-method", "load_data,SurfaceGeometrySource-method" ] }, { "page": "load_fsaverage", "title": "Fetch fsaverage surfaces", "topics": [ "load_fsaverage" ] }, { "page": "load_fsaverage_bundle", "title": "Load a bundle of fsaverage surface variants as a SurfaceSet", "topics": [ "load_fsaverage_bundle" ] }, { "page": "load_fsaverage_std8", "title": "Load fsaverage std.8 surfaces packaged with neurosurf", "topics": [ "load_fsaverage_std8" ] }, { "page": "loadFSSurface", "title": "load Freesurfer ascii surface", "topics": [ "loadFSSurface" ] }, { "page": "loadGIFTISurface", "title": "Load GIFTI surface geometry", "topics": [ "loadGIFTISurface" ] }, { "page": "map_values-NeuroSurface-list-method", "title": "Map Values for NeuroSurface with List Lookup", "topics": [ "map_values,NeuroSurface,list-method" ] }, { "page": "map_values-NeuroSurface-matrix-method", "title": "Map Values for NeuroSurface with Matrix Lookup", "topics": [ "map_values,NeuroSurface,matrix-method" ] }, { "page": "meshToGraph", "title": "Construct a Graph from Mesh Vertices and Faces", "topics": [ "meshToGraph" ] }, { "page": "neighbor_graph-methods", "title": "Construct Neighborhood Graph from Surface Mesh", "topics": [ "neighbor_graph", "neighbor_graph,igraph,numeric,missing,missing-method", "neighbor_graph,SurfaceGeometry,numeric,missing,integer-method", "neighbor_graph,SurfaceGeometry,numeric,missing,missing-method", "neighbor_graph,SurfaceGeometry,numeric,numeric,integer-method", "neighbor_graph,SurfaceGeometry,numeric,numeric,missing-method" ] }, { "page": "neurosurf", "title": "neurosurf: Data structures and IO for surface-based neuroimaging data.", "topics": [ "neurosurf-package", "neurosurf" ] }, { "page": "neurosurf_download_testdata", "title": "Download optional test data for neurosurf", "topics": [ "neurosurf_download_testdata" ] }, { "page": "NeuroSurface", "title": "Construct a NeuroSurface Object", "topics": [ "NeuroSurface" ] }, { "page": "NeuroSurface-class", "title": "NeuroSurface", "topics": [ "NeuroSurface-class" ] }, { "page": "NeuroSurfaceSource-class", "title": "NeuroSurfaceSource Class", "topics": [ "NeuroSurfaceSource", "NeuroSurfaceSource-class" ] }, { "page": "NeuroSurfaceVector", "title": "NeuroSurfaceVector", "topics": [ "NeuroSurfaceVector" ] }, { "page": "NeuroSurfaceVector-class", "title": "NeuroSurfaceVector Class", "topics": [ "NeuroSurfaceVector-class" ] }, { "page": "NeuroSurfaceVectorSource-class", "title": "NeuroSurfaceVectorSource", "topics": [ "NeuroSurfaceVectorSource-class" ] }, { "page": "NIMLSurfaceDataMetaInfo-class", "title": "NIMLSurfaceDataMetaInfo", "topics": [ "NIMLSurfaceDataMetaInfo-class" ] }, { "page": "NIMLSurfaceFileDescriptor-class", "title": "NIMLSurfaceFileDescriptor", "topics": [ "NIMLSurfaceFileDescriptor-class" ] }, { "page": "nodes-methods", "title": "Extract Surface Node Numbers", "topics": [ "nodes", "nodes,NeuroSurface-method", "nodes,NeuroSurfaceVector-method", "nodes,SurfaceGeometry-method" ] }, { "page": "parcel_boundary_contact", "title": "Parcel boundary contact matrix", "topics": [ "parcel_boundary_contact" ] }, { "page": "parcel_geodesic_centroid", "title": "Parcel centroids using geodesic medoids", "topics": [ "parcel_geodesic_centroid" ] }, { "page": "parcel_geodesic_distance_matrix", "title": "Parcel-to-parcel geodesic distances", "topics": [ "parcel_geodesic_distance_matrix" ] }, { "page": "plot_js-methods", "title": "Plot Surface as an HTMLWidget", "topics": [ "plot_js", "plot_js,SurfaceGeometry-method" ] }, { "page": "plot-methods", "title": "Plot a Surface", "topics": [ "plot,ColorMappedNeuroSurface,missing-method", "plot,LabeledNeuroSurface,missing-method", "plot,NeuroSurface,missing-method", "plot,SurfaceGeometry,missing-method", "plot,VertexColoredNeuroSurface,missing-method" ] }, { "page": "plot.neurosurf_plot", "title": "Plot method for neurosurf_plot objects", "topics": [ "plot.neurosurf_plot" ] }, { "page": "plot.SurfaceGeometry", "title": "Plot method for SurfaceGeometry objects", "topics": [ "plot.SurfaceGeometry" ] }, { "page": "plot.SurfaceSet", "title": "Plot method for SurfaceSet objects", "topics": [ "plot.SurfaceSet" ] }, { "page": "print.Searchlight", "title": "Print Method for Searchlight Iterator", "topics": [ "print.Searchlight" ] }, { "page": "projectCoordinates", "title": "Project 3D Coordinates onto a Surface and Smooth the Values", "topics": [ "projectCoordinates" ] }, { "page": "RandomSurfaceSearchlight", "title": "Create a Random Searchlight iterator for surface mesh", "topics": [ "RandomSurfaceSearchlight" ] }, { "page": "read_freesurfer_annot", "title": "Read Freesurfer Annotation File", "topics": [ "read_freesurfer_annot" ] }, { "page": "read_meta_info-methods", "title": "Read Meta Information", "topics": [ "read_meta_info", "read_meta_info,AFNISurfaceFileDescriptor-method", "read_meta_info,FreesurferAsciiSurfaceFileDescriptor-method", "read_meta_info,FreesurferBinarySurfaceFileDescriptor-method", "read_meta_info,GIFTISurfaceFileDescriptor-method", "read_meta_info,NIMLSurfaceFileDescriptor-method" ] }, { "page": "read_surf", "title": "Read Surface Data from a File", "topics": [ "read_surf" ] }, { "page": "read_surf_data", "title": "load surface data and link to 'SurfaceGeometry'", "topics": [ "read_surf_data" ] }, { "page": "read_surf_data_seq", "title": "Read Surface Data Sequence", "topics": [ "read_surf_data_seq" ] }, { "page": "read_surf_geometry", "title": "Read Surface Geometry from File", "topics": [ "read_surf_geometry" ] }, { "page": "remeshSurface", "title": "Remesh a SurfaceGeometry object", "topics": [ "remeshSurface" ] }, { "page": "render_surface_plot", "title": "Render a neurosurf plot using rgl", "topics": [ "render_surface_plot" ] }, { "page": "right-methods", "title": "Get Right Hemisphere", "topics": [ "right", "right,BilatNeuroSurfaceVector-method" ] }, { "page": "ROISurface", "title": "Create an instance of class 'ROISurface'", "topics": [ "ROISurface" ] }, { "page": "ROISurface-class", "title": "ROISurface", "topics": [ "ROISurface-class" ] }, { "page": "ROISurfaceVector", "title": "Create an instance of class 'ROISurfaceVector'", "topics": [ "ROISurfaceVector" ] }, { "page": "ROISurfaceVector-class", "title": "ROISurfaceVector", "topics": [ "ROISurfaceVector-class" ] }, { "page": "sampler_to_triplets", "title": "Extract sparse matrix triplets from a surface sampler", "topics": [ "sampler_to_triplets" ] }, { "page": "series_roi-methods", "title": "Extract ROI Time Series from Surface Vector", "topics": [ "series_roi,NeuroSurfaceVector,numeric-method", "series_roi,NeuroSurfaceVector,ROISurface-method" ] }, { "page": "series-methods", "title": "Extract Time Series from Surface Vector", "topics": [ "series,NeuroSurface,numeric-method", "series,NeuroSurfaceVector,integer-method", "series,NeuroSurfaceVector,numeric-method", "series,NeuroSurfaceVector,ROISurface-method" ] }, { "page": "show_surface_plot", "title": "Show a surface plot in one step", "topics": [ "show_surface_plot" ] }, { "page": "show_surface_widget", "title": "Show an interactive surface widget", "topics": [ "show_surface_widget" ] }, { "page": "show-methods", "title": "show", "topics": [ "show,NeuroSurface-method", "show,NeuroSurfaceVector-method", "show,ROISurface-method", "show,SurfaceDataMetaInfo-method", "show,SurfaceGeometry-method", "show,SurfaceGeometryMetaInfo-method" ] }, { "page": "smooth-methods", "title": "Generic Function for Smoothing a Surface or Associated Data", "topics": [ "smooth", "smooth,SurfaceGeometry-method" ] }, { "page": "smooth-NeuroSurface-method", "title": "Smooth Data on a NeuroSurface Object", "topics": [ "smooth,NeuroSurface-method" ] }, { "page": "snapshot_surface", "title": "Snapshot a surface to a PNG", "topics": [ "snapshot_surface" ] }, { "page": "surf_to_world-methods", "title": "Get Surface-to-World Transform", "topics": [ "surf_to_world", "surf_to_world,SurfaceGeometry-method" ] }, { "page": "surf_to_world-set-methods", "title": "Set Surface-to-World Transform", "topics": [ "surf_to_world<-", "surf_to_world<-,SurfaceGeometry,matrix-method" ] }, { "page": "surface_labels", "title": "List available surface labels", "topics": [ "surface_labels" ] }, { "page": "surface_montage", "title": "Arrange multiple surface views into a single montage figure", "topics": [ "surface_montage" ] }, { "page": "surface_plot", "title": "Create a surface plot specification", "topics": [ "surface_plot" ] }, { "page": "surface_sampler", "title": "Build a reusable surface sampler for multi-frame volumes", "topics": [ "surface_sampler" ] }, { "page": "surface_set", "title": "Construct a SurfaceSet", "topics": [ "surface_set" ] }, { "page": "SurfaceDataMetaInfo-class", "title": "SurfaceDataMetaInfo", "topics": [ "SurfaceDataMetaInfo-class" ] }, { "page": "SurfaceDisk", "title": "Create a Region on Surface", "topics": [ "SurfaceDisk" ] }, { "page": "SurfaceGeometry", "title": "Create a SurfaceGeometry Object", "topics": [ "SurfaceGeometry" ] }, { "page": 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