ROISurfaceVector-class: ROISurfaceVector

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

ROISurfaceVector

Description

A class that respresents a surface-based region of interest

Details

The ROISurfaceVector class extends the concept of ROISurface to handle multiple measurements for each vertex in the region of interest. While ROISurface stores a single value per vertex, ROISurfaceVector stores a matrix of values where each row represents a different measure and each column corresponds to a vertex.

This structure is particularly useful for multivariate analyses of specific brain regions, allowing researchers to:

• Store time series data for each vertex in an ROI

• Maintain multiple modalities of data for the same surface region

• Perform multivariate statistical analyses on regional surface data

• Compare different metrics within the same anatomical region

The data matrix is organized with rows representing different measures and columns representing different vertices, which facilitates efficient access to all measurements for a particular vertex or all vertices for a particular measurement.

Slots

geometry

the geometry of the parent surface: a SurfaceGeometry instance

data

matrix data stored in ROI with number of columns equal to number of coordinates in ROI.

coords

the surface-based coordinates of the data

indices

the nodes of the parent surface stored in the geometry field.

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 the ROI - just using vertices 1 and 2 as an example
roi_indices <- c(1L, 2L)

# Extract coordinates for these vertices
roi_coords <- matrix(
  c(0, 0, 0,  # coordinates for vertex 1
    1, 0, 0), # coordinates for vertex 2
  ncol = 3, byrow = TRUE
)

# Create data matrix for the ROI vertices - 3 different measures
# Each row represents a different measure, each column a different vertex
roi_data <- matrix(
  c(0.75, 1.25,  # values for measure 1
    0.50, 0.80,  # values for measure 2
    0.30, 0.60), # values for measure 3
  nrow = 3, ncol = 2
)

# Create the ROISurfaceVector object
roi_vector <- new("ROISurfaceVector",
                 geometry = geometry,
                 data = roi_data,
                 coords = roi_coords,
                 indices = roi_indices)

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