Setup and Loading Data | Basic Surface Plotting | Coloring Based on Curvature | Overlaying Data Values | Thresholding Data Visualization | Direct Vertex Coloring | Controlling Transparency | Adjusting Lighting and Material | Snapshotting to an image (for knitr/CI) | Changing Viewpoints | Displaying Two Hemispheres | Adding Spheres to the Surface | Plotting Other NeuroSurface Objects | Showing an activation map overlaid on a surface mesh | Showing two hemispheres in same scene | Next Steps
Package: neurosurf 0.1.0
neurosurf: Data Structures and Visualization for Surface-Based Neuroimaging Data
A comprehensive toolkit for working with surface-based neuroimaging data represented as triangle meshes. The package provides classes and methods for creating, manipulating, and visualizing 3D surface geometries (e.g., cortical surfaces), with support for various file formats including FreeSurfer and GIFTI. Key features include: surface smoothing, curvature computation, neighborhood graph construction, geodesic distance calculations, searchlight analysis for surface-based machine learning, and interactive 3D visualization via HTMLWidgets. The package facilitates advanced surface-based analyses through specialized data structures for representing surface geometry and associated functional data.
Authors:
neurosurf_0.1.0.tar.gz
neurosurf_0.1.0.zip(r-4.7)neurosurf_0.1.0.zip(r-4.6)neurosurf_0.1.0.zip(r-4.5)
neurosurf_0.1.0.tgz(r-4.6-x86_64)neurosurf_0.1.0.tgz(r-4.6-arm64)neurosurf_0.1.0.tgz(r-4.5-x86_64)neurosurf_0.1.0.tgz(r-4.5-arm64)
neurosurf_0.1.0.tar.gz(r-4.7-arm64)neurosurf_0.1.0.tar.gz(r-4.7-x86_64)neurosurf_0.1.0.tar.gz(r-4.6-arm64)neurosurf_0.1.0.tar.gz(r-4.6-x86_64)
neurosurf_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
neurosurf/json (API)
| # Install 'neurosurf' in R: |
| install.packages('neurosurf', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bbuchsbaum/neurosurf/issues
Last updated from:1a15009020. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 317 | ||
| linux-devel-x86_64 | OK | 360 | ||
| source / vignettes | OK | 483 | ||
| linux-release-arm64 | OK | 317 | ||
| linux-release-x86_64 | OK | 322 | ||
| macos-release-arm64 | OK | 183 | ||
| macos-release-x86_64 | OK | 440 | ||
| macos-oldrel-arm64 | OK | 134 | ||
| macos-oldrel-x86_64 | OK | 345 | ||
| windows-devel | OK | 253 | ||
| windows-release | OK | 221 | ||
| windows-oldrel | OK | 223 | ||
| wasm-release | OK | 286 |
Exports:add_atlas_outlineadd_surface_layeradd_vector_layeradjacencyapply_surface_samplerArithasas.matrixclear_geodesic_cachecluster_thresholdColorMappedNeuroSurfaceCompareconn_compcoordscurv_colscurv_cols_smoothcurvaturedata_readerdebug_surfwidgetdraw_surface_plotexample_surface_geometryfacesfind_all_neighborsfind_nearest_vertexfind_roi_boundariesfindBoundariesgaussian_splatgaussian_splat_multigaussian_splat_vertexgeodesic_distance_matrixgeodesic_distancesgeometryget_surfacegraphindiceslaplacianleftload_dataload_fsaverageload_fsaverage_bundleload_fsaverage_std8loadFSSurfaceloadGIFTISurfacemap_valuesmeshToGraphneighbor_graphneurosurf_download_testdataNeuroSurfaceNeuroSurfaceSourceNeuroSurfaceVectornodesparcel_boundary_contactparcel_geodesic_centroidparcel_geodesic_distance_matrixplotplot_jsprojectCoordinatesRandomSurfaceSearchlightread_freesurfer_annotread_meta_inforead_surfread_surf_dataread_surf_data_seqread_surf_geometryremeshSurfacerender_surface_plotrenderSurfwidgetrightROISurfaceROISurfaceVectorsampler_to_tripletsseriesseries_roishowshow_surface_plotshow_surface_widgetsmoothsnapshot_surfacesurf_to_worldsurf_to_world<-surface_labelssurface_montagesurface_plotsurface_samplersurface_setSurfaceDiskSurfaceGeometrySurfaceSearchlightsurfwidgetsurfwidgetOutputupdateAlphaupdateColorMapupdateIRangeupdateRotationSpeedupdateThresholdupdateVertexColorsupdateZoomvaluesVertexColoredNeuroSurfaceverticesview_surfacevol_to_surfvol_to_surf_sdfwrite_surf_data
Dependencies:assertthatbase64encbigassertrbigparallelrbigstatsrbitbit64bitopsbslibcachemcaToolsclicliprcodetoolscolorplanecowplotcpp11crayondbscandeflistdigestdoParallelevaluatefarverfastmapffflockFNNfontawesomeforeachfsfuturefuture.applygenericsggplot2giftiglobalsgluegplotsgtablegtoolshighrhmshtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelistenvmagrittrMatrixmemoisemimemmapneuroim2parallellypatchworkpillarpkgconfigplyrpngprettyunitsprogresspspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadrrglRhpcBLASctlrlangrmarkdownrmioRNiftiRNiftyRegroptimRSpectraRvcgS7sassscalesstringistringrtibbletidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxml2yaml
Displaying Surfaces with RGL
Last update: 2026-05-31
Started: 2019-11-23
Interactive Surface Visualization with surfwidget
Introduction | Quick Start | Basic Surface Display | Data Visualization | Advanced Configuration | Vertex-Colored Surfaces | Interactive Controls | Troubleshooting | Advantages over Static Plots | Next Steps
Last update: 2026-05-31
Started: 2025-08-20
Introduction to NeuroSurf Data Structures
Setup | SurfaceGeometry: Representing the Mesh | Loading a SurfaceGeometry | Accessing Geometry Properties | NeuroSurface: Mapping Data to Geometry | Creating a NeuroSurface | Loading Data with read_surf (Optional Data File) | Accessing NeuroSurface Properties | NeuroSurfaceVector: Mapping Multiple Data Vectors | Creating a NeuroSurfaceVector | Accessing NeuroSurfaceVector Properties | Specialized NeuroSurface Classes | Next Steps
Last update: 2026-05-31
Started: 2025-05-28
Publication-quality surface figures
Load surfaces and an atlas | A continuous overlay with a colourbar | Adding atlas outlines | Next Steps
Last update: 2026-05-31
Started: 2026-05-31
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract All Data from NeuroSurfaceVector | [,NeuroSurfaceVector,missing,missing,ANY-method |
| Subset NeuroSurfaceVector by Column | [,NeuroSurfaceVector,missing,numeric,ANY-method |
| Subset NeuroSurfaceVector by Row | [,NeuroSurfaceVector,numeric,missing,ANY-method |
| Subset NeuroSurfaceVector | [,NeuroSurfaceVector,numeric,numeric,ANY-method |
| Subset an ROISurface Object | [,ROISurface,numeric,missing,ANY-method |
| Extract Data from NeuroSurfaceVector | [[,NeuroSurfaceVector,numeric-method |
| Add an atlas outline layer to a surface plot | add_atlas_outline |
| Add a data layer to a surface plot | add_surface_layer |
| Add a vector field overlay | add_vector_layer |
| Get Adjacency Graph | adjacency adjacency,SurfaceGeometry,character-method adjacency,SurfaceGeometry,missing-method adjacency,SurfaceGeometry,numeric-method |
| AFNISurfaceFileDescriptor | AFNISurfaceFileDescriptor-class |
| Apply a precomputed surface sampler to a volume | apply_surface_sampler |
| Arithmetic Operations for NeuroSurface Objects | Arith,NeuroSurface,NeuroSurface-method Arith,NeuroSurface,NeuroSurfaceVector-method Arith,NeuroSurface,numeric-method Arith,numeric,NeuroSurface-method |
| Arithmetic Operations for NeuroSurfaceVector Objects | Arith,NeuroSurfaceVector,NeuroSurface-method Arith,NeuroSurfaceVector,NeuroSurfaceVector-method Arith,NeuroSurfaceVector,numeric-method Arith,numeric,NeuroSurfaceVector-method |
| Coercion Methods for NeuroSurface Objects | as |
| Convert Surface Data to Matrix | as.matrix,BilatNeuroSurfaceVector-method as.matrix,NeuroSurfaceVector-method as.matrix,ROISurfaceVector-method |
| Convert Surface Data to Vector | as.vector,NeuroSurface-method |
| Bilateral NeuroSurface Vector Class | BilatNeuroSurfaceVector-class |
| Clear geodesic cache | clear_geodesic_cache |
| Apply Cluster-Extent Threshold to Surface Data | cluster_threshold cluster_threshold,NeuroSurface-method cluster_threshold,NeuroSurfaceVector-method |
| ColorMappedNeuroSurface | ColorMappedNeuroSurface |
| ColorMappedNeuroSurface | ColorMappedNeuroSurface-class |
| Comparison Operations for NeuroSurface Objects | Compare,NeuroSurface,NeuroSurface-method |
| Comparison Operations for NeuroSurface Objects | Compare,NeuroSurface,numeric-method |
| Comparison Operations for NeuroSurfaceVector Objects | Compare,NeuroSurfaceVector,NeuroSurfaceVector-method Compare,NeuroSurfaceVector,numeric-method Compare,numeric,NeuroSurfaceVector-method |
| Compute boundary hull points in world space (C++) | compute_hull_world_cpp |
| Compute Connected Components on a Surface | conn_comp,NeuroSurface-method conn_comp,NeuroSurfaceVector-method |
| Extract Vertex Coordinates | coords,igraph-method coords,NeuroSurface-method coords,NeuroSurfaceVector-method coords,ROISurface-method coords,SurfaceGeometry-method |
| Convert Curvature Values to Binary Colors for Visualization | curv_cols |
| Convert Curvature Values to Smooth Gradient Colors | curv_cols_smooth |
| Compute Surface Curvature Vector | curv curvature curvature,SurfaceGeometry-method |
| Create a Column Reader for Surface Data | data_reader,NIMLSurfaceDataMetaInfo-method data_reader,SurfaceGeometryMetaInfo-method |
| Debugging Helper for surfwidget | debug_surfwidget |
| Draw a static multi-panel surface figure | draw_surface_plot |
| Extract Faces from a Surface Object | faces faces,NeuroSurface-method faces,NeuroSurfaceVector-method faces,SurfaceGeometry-method |
| Find Node Neighbors in a Surface Mesh | find_all_neighbors |
| Find the nearest surface vertex to a 3D point | find_nearest_vertex |
| Find boundaries of ROIs on a surface mesh | find_roi_boundaries |
| Find Boundaries Between Regions on a Surface | findBoundaries findBoundaries,NeuroSurface-method |
| FresurferAsciiSurfaceFileDescriptor | FreesurferAsciiSurfaceFileDescriptor-class |
| FresurferBinarySurfaceFileDescriptor | FreesurferBinarySurfaceFileDescriptor-class |
| FreesurferSurfaceGeometryMetaInfo Class | FreesurferSurfaceGeometryMetaInfo-class |
| Gaussian splats on surface meshes | gaussian_splat gaussian_splat_multi gaussian_splat_vertex |
| All-pairs geodesic distance matrix (chunked) | geodesic_distance_matrix |
| Geodesic distances from sources to targets | geodesic_distances |
| Extract Geometry from Surface Object | geometry geometry,NeuroSurface-method geometry,NeuroSurfaceVector-method |
| Retrieve a geometry from a SurfaceSet | get_surface |
| GIFTISurfaceDataMetaInfo | GIFTISurfaceDataMetaInfo-class |
| GIFTISurfaceFileDescriptor | GIFTISurfaceFileDescriptor-class |
| GIFTISurfaceGeometryMetaInfo | GIFTISurfaceGeometryMetaInfo-class |
| extract 'igraph' object | graph graph,NeuroSurface-method graph,NeuroSurfaceVector-method graph,SurfaceGeometry-method |
| Extract Vertex Indices | indices,NeuroSurface-method indices,NeuroSurfaceVector-method indices,ROISurface-method indices,ROISurfaceVector-method |
| LabeledNeuroSurface Class | LabeledNeuroSurface-class |
| Compute Graph Laplacian | laplacian laplacian,SurfaceGeometry,missing,missing-method laplacian,SurfaceGeometry,missing,numeric-method |
| Get Left Hemisphere | left left,BilatNeuroSurfaceVector-method |
| Get Length of Surface Object | length,ROISurface-method |
| load_data | load_data,FreesurferSurfaceGeometryMetaInfo-method load_data,GIFTISurfaceGeometryMetaInfo-method load_data,NeuroSurfaceSource-method load_data,NeuroSurfaceVectorSource-method load_data,SurfaceGeometrySource-method |
| Fetch fsaverage surfaces | load_fsaverage |
| Load a bundle of fsaverage surface variants as a SurfaceSet | load_fsaverage_bundle |
| Load fsaverage std.8 surfaces packaged with neurosurf | load_fsaverage_std8 |
| load Freesurfer ascii surface | loadFSSurface |
| Load GIFTI surface geometry | loadGIFTISurface |
| Map Values for NeuroSurface with List Lookup | map_values,NeuroSurface,list-method |
| Map Values for NeuroSurface with Matrix Lookup | map_values,NeuroSurface,matrix-method |
| Construct a Graph from Mesh Vertices and Faces | meshToGraph |
| Construct Neighborhood Graph from Surface Mesh | 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 |
| neurosurf: Data structures and IO for surface-based neuroimaging data. | neurosurf-package neurosurf |
| Download optional test data for neurosurf | neurosurf_download_testdata |
| Construct a NeuroSurface Object | NeuroSurface |
| NeuroSurface | NeuroSurface-class |
| NeuroSurfaceSource Class | NeuroSurfaceSource NeuroSurfaceSource-class |
| NeuroSurfaceVector | NeuroSurfaceVector |
| NeuroSurfaceVector Class | NeuroSurfaceVector-class |
| NeuroSurfaceVectorSource | NeuroSurfaceVectorSource-class |
| NIMLSurfaceDataMetaInfo | NIMLSurfaceDataMetaInfo-class |
| NIMLSurfaceFileDescriptor | NIMLSurfaceFileDescriptor-class |
| Extract Surface Node Numbers | nodes nodes,NeuroSurface-method nodes,NeuroSurfaceVector-method nodes,SurfaceGeometry-method |
| Parcel boundary contact matrix | parcel_boundary_contact |
| Parcel centroids using geodesic medoids | parcel_geodesic_centroid |
| Parcel-to-parcel geodesic distances | parcel_geodesic_distance_matrix |
| Plot Surface as an HTMLWidget | plot_js plot_js,SurfaceGeometry-method |
| Plot a Surface | plot,ColorMappedNeuroSurface,missing-method plot,LabeledNeuroSurface,missing-method plot,NeuroSurface,missing-method plot,SurfaceGeometry,missing-method plot,VertexColoredNeuroSurface,missing-method |
| Plot method for neurosurf_plot objects | plot.neurosurf_plot |
| Plot method for SurfaceGeometry objects | plot.SurfaceGeometry |
| Plot method for SurfaceSet objects | plot.SurfaceSet |
| Print Method for Searchlight Iterator | print.Searchlight |
| Project 3D Coordinates onto a Surface and Smooth the Values | projectCoordinates |
| Create a Random Searchlight iterator for surface mesh | RandomSurfaceSearchlight |
| Read Freesurfer Annotation File | read_freesurfer_annot |
| Read Meta Information | 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 |
| Read Surface Data from a File | read_surf |
| load surface data and link to 'SurfaceGeometry' | read_surf_data |
| Read Surface Data Sequence | read_surf_data_seq |
| Read Surface Geometry from File | read_surf_geometry |
| Remesh a SurfaceGeometry object | remeshSurface |
| Render a neurosurf plot using rgl | render_surface_plot |
| Get Right Hemisphere | right right,BilatNeuroSurfaceVector-method |
| Create an instance of class 'ROISurface' | ROISurface |
| ROISurface | ROISurface-class |
| Create an instance of class 'ROISurfaceVector' | ROISurfaceVector |
| ROISurfaceVector | ROISurfaceVector-class |
| Extract sparse matrix triplets from a surface sampler | sampler_to_triplets |
| Extract ROI Time Series from Surface Vector | series_roi,NeuroSurfaceVector,numeric-method series_roi,NeuroSurfaceVector,ROISurface-method |
| Extract Time Series from Surface Vector | series,NeuroSurface,numeric-method series,NeuroSurfaceVector,integer-method series,NeuroSurfaceVector,numeric-method series,NeuroSurfaceVector,ROISurface-method |
| Show a surface plot in one step | show_surface_plot |
| Show an interactive surface widget | show_surface_widget |
| show | show,NeuroSurface-method show,NeuroSurfaceVector-method show,ROISurface-method show,SurfaceDataMetaInfo-method show,SurfaceGeometry-method show,SurfaceGeometryMetaInfo-method |
| Generic Function for Smoothing a Surface or Associated Data | smooth smooth,SurfaceGeometry-method |
| Smooth Data on a NeuroSurface Object | smooth,NeuroSurface-method |
| Snapshot a surface to a PNG | snapshot_surface |
| Get Surface-to-World Transform | surf_to_world surf_to_world,SurfaceGeometry-method |
| Set Surface-to-World Transform | surf_to_world<- surf_to_world<-,SurfaceGeometry,matrix-method |
| List available surface labels | surface_labels |
| Arrange multiple surface views into a single montage figure | surface_montage |
| Create a surface plot specification | surface_plot |
| Build a reusable surface sampler for multi-frame volumes | surface_sampler |
| Construct a SurfaceSet | surface_set |
| SurfaceDataMetaInfo | SurfaceDataMetaInfo-class |
| Create a Region on Surface | SurfaceDisk |
| Create a SurfaceGeometry Object | SurfaceGeometry |
| SurfaceGeometry Class | SurfaceGeometry-class |
| SurfaceGeometryMetaInfo Class | SurfaceGeometryMetaInfo-class |
| SurfaceGeometrySource Class | SurfaceGeometrySource-class |
| SurfaceSearchlight | SurfaceSearchlight |
| SurfaceSet: bundle multiple surface variants for one hemisphere | curvature,SurfaceSet-method faces,SurfaceSet-method geometry,SurfaceSet-method graph,SurfaceSet-method nodes,SurfaceSet-method SurfaceSet-class vertices,SurfaceSet-method |
| Create a Surface Widget | surfwidget surfwidget,ColorMappedNeuroSurface-method surfwidget,NeuroSurface-method surfwidget,SurfaceGeometry-method surfwidget,VertexColoredNeuroSurface-method |
| Update Surface Color Map | updateColorMap |
| Extract Data Values from Surface Objects | values,NeuroSurface-method values,ROISurface-method values,ROISurfaceVector-method |
| VertexColoredNeuroSurface | VertexColoredNeuroSurface |
| VertexColoredNeuroSurface | VertexColoredNeuroSurface-class |
| VertexData | VertexData-class |
| Extract Vertices from a Surface Object | vertices vertices,NeuroSurface-method vertices,NeuroSurfaceVector-method vertices,SurfaceGeometry-method |
| Display a 3D Brain Surface using RGL | view_surface |
| Map values from a 3D volume to a surface in the same coordinate space | vol_to_surf |
| Map a volume to surface after SDF-based rigid alignment | vol_to_surf_sdf |
| Write Surface Data to File | write_surf_data |
