NeuroSurfaceSource-class: NeuroSurfaceSource Class

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

NeuroSurfaceSource Class

Description

The 'NeuroSurfaceSource' class serves as a factory for creating NeuroSurface instances. It encapsulates all necessary information to construct a neuroimaging surface, including geometry, metadata, and indexing information.

Usage

NeuroSurfaceSource(
  surface_geom,
  surface_data_name,
  colind = NULL,
  nodeind = NULL
)

Arguments

surface_geom	the name of the file containing the surface geometry or a SurfaceGeometry instance
surface_data_name	the name of the file containing the data values to be mapped to the surface.
colind	the subset of column indices to load from surface data matrix (if provided)
nodeind	the subset of node indices to load from surface data matrix (if provided)

Details

This class is designed to facilitate the creation of NeuroSurface objects by providing a standardized way to store and access all required components. It combines geometric information, metadata, and indexing details necessary for constructing a complete neuroimaging surface representation.

Value

An object of class NeuroSurfaceSource or NeuroSurfaceVectorSource that contains information about the surface geometry and associated data. If the data has multiple columns (colind > 1), a NeuroSurfaceVectorSource is returned; otherwise, a NeuroSurfaceSource is returned. These objects can be used to load and map neuroimaging data onto brain surfaces.

Slots

geometry

An object of class SurfaceGeometry representing the underlying surface structure.

data_meta_info

An object of class SurfaceDataMetaInfo containing metadata about the surface data.

colind

An integer specifying the column index of the surface map to be loaded.

nodeind

An integer vector specifying the node indices of the surface map to be loaded.

See Also

NeuroSurface, SurfaceGeometry, SurfaceDataMetaInfo

Examples

# Create a simple 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")

# Create a SurfaceDataMetaInfo object
data_meta_info <- new("SurfaceDataMetaInfo",
                      header_file = "data_meta.txt",
                      data_file = "surface_data.1D",
                      file_descriptor = new("FileFormat"),
                      node_count = 4L,
                      nels = 1L,
                      label = "thickness")

# Create a NeuroSurfaceSource object
neuro_source <- new("NeuroSurfaceSource",
                    geometry = geometry,
                    data_meta_info = data_meta_info,
                    colind = 1L,
                    nodeind = 1:4)

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