ROISurface-class: ROISurface

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

ROISurface

Description

A class that respresents a surface-based region of interest

Details

The ROISurface class provides a way to represent a specific subset of vertices on a brain surface along with their associated data values. This is particularly useful for analyzing or visualizing specific anatomical or functional regions on the cortical surface.

The class maintains a reference to the complete parent surface geometry while storing only the relevant subset of vertices, their coordinates, and their data values. The indices slot allows mapping back to the original vertex indices in the parent surface.

Typical use cases include:

• Extracting and analyzing data from anatomical regions of interest

• Working with functional clusters identified in analyses

• Isolating specific surface features for detailed investigation

• Statistical analysis of data within defined surface regions

Slots

geometry

the geometry of the parent surface: a SurfaceGeometry instance

data

the vector-valued numeric data stored in ROI

coords

the surface-based coordinates of the data

indices

the node indices 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 values for the ROI vertices
roi_data <- c(0.75, 1.25)  # example values for the two vertices

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

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