Package index • neurosurf

read surfaces

read different surface files into R

read_surf(): Read Surface Data from a File
read_surf_data(): load surface data and link to SurfaceGeometry
read_surf_data_seq(): Read Surface Data Sequence
read_freesurfer_annot(): Read Freesurfer Annotation File
read_surf_geometry(): Read Surface Geometry from File
write_surf_data(): Write Surface Data to File

surface-based operations and functions

process of manipulate surface data and geometry

smooth(): Generic Function for Smoothing a Surface or Associated Data
cluster_threshold(): Apply Cluster-Extent Threshold to Surface Data
curvature(): Compute Surface Curvature Vector

extractors

extract infromation from surface data structures

vertices(): Extract Vertices from a Surface Object
nodes(): Extract Surface Node Numbers
geometry(): Extract Geometry from Surface Object
graph(): extract igraph object
left(): Get Left Hemisphere
right(): Get Right Hemisphere
adjacency(): Get Adjacency Graph
laplacian(): Compute Graph Laplacian

Complete reference

Catch-all index to include any remaining topics.

AFNISurfaceFileDescriptor-class: AFNISurfaceFileDescriptor
Arith(<NeuroSurface>,<NeuroSurface>) Arith(<NeuroSurface>,<numeric>) Arith(<numeric>,<NeuroSurface>) Arith(<NeuroSurface>,<NeuroSurfaceVector>): Arithmetic Operations for NeuroSurface Objects
Arith(<NeuroSurfaceVector>,<NeuroSurfaceVector>) Arith(<NeuroSurfaceVector>,<numeric>) Arith(<numeric>,<NeuroSurfaceVector>) Arith(<NeuroSurfaceVector>,<NeuroSurface>): Arithmetic Operations for NeuroSurfaceVector Objects
BilatNeuroSurfaceVector-class: Bilateral NeuroSurface Vector Class
ColorMappedNeuroSurface-class: ColorMappedNeuroSurface
ColorMappedNeuroSurface(): ColorMappedNeuroSurface
Compare(<NeuroSurface>,<NeuroSurface>): Comparison Operations for NeuroSurface Objects
Compare(<NeuroSurface>,<numeric>): Comparison Operations for NeuroSurface Objects
Compare(<NeuroSurfaceVector>,<NeuroSurfaceVector>) Compare(<NeuroSurfaceVector>,<numeric>) Compare(<numeric>,<NeuroSurfaceVector>): Comparison Operations for NeuroSurfaceVector Objects
FreesurferAsciiSurfaceFileDescriptor-class: FresurferAsciiSurfaceFileDescriptor
FreesurferBinarySurfaceFileDescriptor-class: FresurferBinarySurfaceFileDescriptor
FreesurferSurfaceGeometryMetaInfo-class: FreesurferSurfaceGeometryMetaInfo Class
GIFTISurfaceDataMetaInfo-class: GIFTISurfaceDataMetaInfo
GIFTISurfaceFileDescriptor-class: GIFTISurfaceFileDescriptor
GIFTISurfaceGeometryMetaInfo-class: GIFTISurfaceGeometryMetaInfo
LabeledNeuroSurface-class: LabeledNeuroSurface Class
NIMLSurfaceDataMetaInfo-class: NIMLSurfaceDataMetaInfo
NIMLSurfaceFileDescriptor-class: NIMLSurfaceFileDescriptor
NeuroSurface-class: NeuroSurface
NeuroSurface(): Construct a NeuroSurface Object
NeuroSurfaceSource(): NeuroSurfaceSource Class
NeuroSurfaceVector-class: NeuroSurfaceVector Class
NeuroSurfaceVector(): NeuroSurfaceVector
NeuroSurfaceVectorSource-class: NeuroSurfaceVectorSource
ROISurface-class: ROISurface
ROISurface(): Create an instance of class ROISurface
ROISurfaceVector-class: ROISurfaceVector
ROISurfaceVector(): Create an instance of class ROISurfaceVector
RandomSurfaceSearchlight(): Create a Random Searchlight iterator for surface mesh
SurfaceDataMetaInfo-class: SurfaceDataMetaInfo
SurfaceDisk(): Create a Region on Surface
SurfaceGeometry-class: SurfaceGeometry Class
SurfaceGeometry(): Create a SurfaceGeometry Object
SurfaceGeometryMetaInfo-class: SurfaceGeometryMetaInfo Class
SurfaceGeometrySource-class: SurfaceGeometrySource Class
SurfaceSearchlight(): SurfaceSearchlight
geometry(<SurfaceSet>) vertices(<SurfaceSet>) faces(<SurfaceSet>) nodes(<SurfaceSet>) graph(<SurfaceSet>) curvature(<SurfaceSet>): SurfaceSet: bundle multiple surface variants for one hemisphere
VertexColoredNeuroSurface-class: VertexColoredNeuroSurface
VertexColoredNeuroSurface(): VertexColoredNeuroSurface
VertexData-class: VertexData
add_atlas_outline(): Add an atlas outline layer to a surface plot
add_surface_layer(): Add a data layer to a surface plot
add_vector_layer(): Add a vector field overlay
adjacency(): Get Adjacency Graph
apply_surface_sampler(): Apply a precomputed surface sampler to a volume
as: Coercion Methods for NeuroSurface Objects
as.matrix(<ROISurfaceVector>) as.matrix(<NeuroSurfaceVector>) as.matrix(<BilatNeuroSurfaceVector>): Convert Surface Data to Matrix
as.vector(<NeuroSurface>): Convert Surface Data to Vector
clear_geodesic_cache(): Clear geodesic cache
cluster_threshold(): Apply Cluster-Extent Threshold to Surface Data
compute_hull_world_cpp(): Compute boundary hull points in world space (C++)
conn_comp(<NeuroSurfaceVector>) conn_comp(<NeuroSurface>): Compute Connected Components on a Surface
coords(<ROISurface>) coords(<SurfaceGeometry>) coords(<igraph>) coords(<NeuroSurfaceVector>) coords(<NeuroSurface>): Extract Vertex Coordinates
curv_cols(): Convert Curvature Values to Binary Colors for Visualization
curvature(): Compute Surface Curvature Vector
data_reader(<SurfaceGeometryMetaInfo>) data_reader(<NIMLSurfaceDataMetaInfo>): Create a Column Reader for Surface Data
debug_surfwidget(): Debugging Helper for surfwidget
draw_surface_plot(): Draw a static multi-panel surface figure
faces(): Extract Faces from a Surface Object
findBoundaries(): Find Boundaries Between Regions on a Surface
find_all_neighbors(): Find Node Neighbors in a Surface Mesh
find_nearest_vertex(): Find the nearest surface vertex to a 3D point
find_roi_boundaries(): Find boundaries of ROIs on a surface mesh
gaussian_splat() gaussian_splat_vertex() gaussian_splat_multi(): Gaussian splats on surface meshes
geodesic_distance_matrix(): All-pairs geodesic distance matrix (chunked)
geodesic_distances(): Geodesic distances from sources to targets
geometry(): Extract Geometry from Surface Object
get_surface(): Retrieve a geometry from a SurfaceSet
graph(): extract igraph object
indices(<ROISurface>) indices(<ROISurfaceVector>) indices(<NeuroSurfaceVector>) indices(<NeuroSurface>): Extract Vertex Indices
laplacian(): Compute Graph Laplacian
left(): Get Left Hemisphere
length(<ROISurface>): Get Length of Surface Object
loadFSSurface(): load Freesurfer ascii surface
loadGIFTISurface(): Load GIFTI surface geometry
load_data(<NeuroSurfaceVectorSource>) load_data(<NeuroSurfaceSource>) load_data(<FreesurferSurfaceGeometryMetaInfo>) load_data(<GIFTISurfaceGeometryMetaInfo>) load_data(<SurfaceGeometrySource>): load_data
load_fsaverage(): Fetch fsaverage surfaces
load_fsaverage_bundle(): Load a bundle of fsaverage surface variants as a SurfaceSet
load_fsaverage_std8(): Load fsaverage std.8 surfaces packaged with neurosurf
map_values(<NeuroSurface>,<list>): Map Values for NeuroSurface with List Lookup
map_values(<NeuroSurface>,<matrix>): Map Values for NeuroSurface with Matrix Lookup
meshToGraph(): Construct a Graph from Mesh Vertices and Faces
neighbor_graph(): Construct Neighborhood Graph from Surface Mesh
neurosurf-package neurosurf: neurosurf: Data structures and IO for surface-based neuroimaging data.
neurosurf_download_testdata(): Download optional test data for neurosurf
nodes(): Extract Surface Node Numbers
parcel_boundary_contact(): Parcel boundary contact matrix
parcel_geodesic_centroid(): Parcel centroids using geodesic medoids
parcel_geodesic_distance_matrix(): Parcel-to-parcel geodesic distances
plot(<SurfaceGeometry>,<missing>) plot(<NeuroSurface>,<missing>) plot(<LabeledNeuroSurface>,<missing>) plot(<ColorMappedNeuroSurface>,<missing>) plot(<VertexColoredNeuroSurface>,<missing>): Plot a Surface
plot(<SurfaceGeometry>): Plot method for SurfaceGeometry objects
plot(<SurfaceSet>): Plot method for SurfaceSet objects
plot(<neurosurf_plot>): Plot method for neurosurf_plot objects
plot_js(): Plot Surface as an HTMLWidget
print(<Searchlight>): Print Method for Searchlight Iterator
projectCoordinates(): Project 3D Coordinates onto a Surface and Smooth the Values
read_freesurfer_annot(): Read Freesurfer Annotation File
read_meta_info(<AFNISurfaceFileDescriptor>) read_meta_info(<NIMLSurfaceFileDescriptor>) read_meta_info(<FreesurferAsciiSurfaceFileDescriptor>) read_meta_info(<FreesurferBinarySurfaceFileDescriptor>) read_meta_info(<GIFTISurfaceFileDescriptor>): Read Meta Information
read_surf(): Read Surface Data from a File
read_surf_data(): load surface data and link to SurfaceGeometry
read_surf_data_seq(): Read Surface Data Sequence
read_surf_geometry(): Read Surface Geometry from File
remeshSurface(): Remesh a SurfaceGeometry object
render_surface_plot(): Render a neurosurf plot using rgl
right(): Get Right Hemisphere
sampler_to_triplets(): Extract sparse matrix triplets from a surface sampler
series(<NeuroSurfaceVector>,<numeric>) series(<NeuroSurfaceVector>,<integer>) series(<NeuroSurfaceVector>,<ROISurface>) series(<NeuroSurface>,<numeric>): Extract Time Series from Surface Vector
series_roi(<NeuroSurfaceVector>,<numeric>) series_roi(<NeuroSurfaceVector>,<ROISurface>): Extract ROI Time Series from Surface Vector
show(<SurfaceGeometryMetaInfo>) show(<SurfaceDataMetaInfo>) show(<ROISurface>) show(<SurfaceGeometry>) show(<NeuroSurfaceVector>) show(<NeuroSurface>): show
show_surface_plot(): Show a surface plot in one step
show_surface_widget(): Show an interactive surface widget
smooth(<NeuroSurface>): Smooth Data on a NeuroSurface Object
smooth(): Generic Function for Smoothing a Surface or Associated Data
snapshot_surface(): Snapshot a surface to a PNG
`[`(<NeuroSurfaceVector>,<missing>,<missing>,<ANY>): Extract All Data from NeuroSurfaceVector
`[`(<NeuroSurfaceVector>,<missing>,<numeric>,<ANY>): Subset NeuroSurfaceVector by Column
`[`(<NeuroSurfaceVector>,<numeric>,<missing>,<ANY>): Subset NeuroSurfaceVector by Row
`[`(<NeuroSurfaceVector>,<numeric>,<numeric>,<ANY>): Subset NeuroSurfaceVector
`[`(<ROISurface>,<numeric>,<missing>,<ANY>): Subset an ROISurface Object
`[[`(<NeuroSurfaceVector>,<numeric>): Extract Data from NeuroSurfaceVector
surf_to_world(): Get Surface-to-World Transform
`surf_to_world<-`(): Set Surface-to-World Transform
surface_labels(): List available surface labels
surface_plot(): Create a surface plot specification
surface_sampler(): Build a reusable surface sampler for multi-frame volumes
surface_set(): Construct a SurfaceSet
surfwidget(): Create a Surface Widget
updateColorMap(): Update Surface Color Map
values(<ROISurface>) values(<ROISurfaceVector>) values(<NeuroSurface>): Extract Data Values from Surface Objects
vertices(): Extract Vertices from a Surface Object
view_surface(): Display a 3D Brain Surface using RGL
vol_to_surf(): Map values from a 3D volume to a surface in the same coordinate space
vol_to_surf_sdf(): Map a volume to surface after SDF-based rigid alignment
write_surf_data(): Write Surface Data to File