LabeledNeuroSurface-class: LabeledNeuroSurface Class

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

LabeledNeuroSurface Class

Description

Represents a 3D surface with labeled vertices, extending NeuroSurface.

Details

The LabeledNeuroSurface class provides a way to represent anatomical parcellations or other categorical divisions of a brain surface. Each vertex is assigned a label based on its data value, which typically represents a region ID. The class maintains a mapping between these IDs and human-readable labels, along with colors for visualization.

This is particularly useful for displaying anatomical atlases or the results of clustering algorithms on the brain surface.

Slots

labels

Character vector of label annotations

cols

Character vector of hex color codes for labels

See Also

NeuroSurface

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(1, 2, 1, 3)  # Values representing region IDs

# Define the unique labels for the regions
labels <- c("Region A", "Region B", "Region C")

# Define colors for each label (in the same order as labels)
colors <- c("#FF0000", "#00FF00", "#0000FF")  # Red, Green, Blue

# Create the LabeledNeuroSurface object
labeled_surface <- new("LabeledNeuroSurface",
                      geometry = geometry,
                      indices = indices,
                      data = vertex_data,
                      labels = labels,
                      cols = colors)

# In this example, vertices are labeled as follows:
# - Vertices 1 and 3 belong to "Region A" (Red)
# - Vertex 2 belongs to "Region B" (Green)
# - Vertex 4 belongs to "Region C" (Blue)

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