NeuroSurface-class: NeuroSurface

In bbuchsbaum/neurosurf: Data structures and visualization for surface-based neuroimaging data

NeuroSurface

Description

a three-dimensional surface consisting of a set of triangle vertices with one value per vertex.

Details

The NeuroSurface class is a fundamental representation of surface-based neuroimaging data. It combines geometric information about a brain surface with data values mapped to each vertex of that surface.

The class consists of three core components:

• geometry: The underlying 3D surface structure, containing vertex coordinates, face definitions, and topological information

• indices: Identifiers for the subset of vertices in the geometry that have associated data values

• data: A numeric vector containing one value per vertex, representing measurements such as cortical thickness, functional activation, or any other surface-mapped metric

This class serves as the foundation for more specialized surface representations like ColorMappedNeuroSurface, VertexColoredNeuroSurface, and LabeledNeuroSurface. It facilitates common operations such as visualization, statistical analysis, and spatial processing of surface-based neuroimaging data.

Slots

geometry

the surface geometry, an instance of SurfaceGeometry

indices

an integer vector specifying the subset of valid surface nodes encoded in the geometry object.

data

the 1-D vector of data value at each vertex of the mesh

Examples

# Create a simple tetrahedron mesh for the example
vertices <- c(
  0, 0, 0,
  1, 0, 0,
  0, 1, 0,
  0, 0, 1
)
triangles <- c(
  1, 2, 3,
  1, 2, 4,
  1, 3, 4,
  2, 3, 4
)

# Create mesh3d object
mesh <- rgl::mesh3d(vertices = vertices, triangles = triangles)

# Create a graph representation
edges <- rbind(
  c(1,2), c(1,3), c(1,4),
  c(2,3), c(2,4),
  c(3,4)
)
graph <- igraph::graph_from_edgelist(edges)

# Create a SurfaceGeometry object
geometry <- new("SurfaceGeometry",
               mesh = mesh,
               graph = graph,
               hemi = "left")

# Define indices for all vertices
indices <- 1:4

# Create data values for each vertex
vertex_data <- c(0.5, 1.2, 0.8, 1.5)  # example values for the vertices

# Create the NeuroSurface object
neuro_surface <- new("NeuroSurface",
                    geometry = geometry,
                    indices = indices,
                    data = vertex_data)

# The data values are now mapped to the surface vertices
# and can be visualized or analyzed

bbuchsbaum/neurosurf documentation built on June 10, 2025, 8:22 p.m.