spherical_roi: Create a Spherical Region of Interest

In neuroim2: Data Structures for Brain Imaging Data

Create a Spherical Region of Interest

Description

Creates a Spherical ROI based on a centroid.

Usage

spherical_roi(
  bvol,
  centroid,
  radius,
  fill = NULL,
  nonzero = FALSE,
  use_cpp = TRUE
)

Arguments

bvol	an NeuroVol or NeuroSpace instance
centroid	the center of the sphere in positive-coordinate (i,j,k) voxel space.
radius	the radius in real units (e.g. millimeters) of the spherical ROI
fill	optional value(s) to store as data
nonzero	if TRUE, keep only nonzero elements from bvol
use_cpp	whether to use compiled c++ code

Value

an instance of class ROIVol

See Also

[spherical_roi_set()] for efficiently creating many spherical ROIs, [series_roi()] and [coords()] for extracting time series and coordinates from ROIs, and the vignette: vignette("regionOfInterest", package = "neuroim2").

Examples

 sp1 <- NeuroSpace(c(10,10,10), c(1,2,3))
 # create an ROI centered around the integer-valued positive voxel coordinate: i=5, j=5, k=5
 cube <- spherical_roi(sp1, c(5,5,5), 3.5)
 vox <- coords(cube)
 cds <- coords(cube, real=TRUE)
 ## fill in ROI with value of 6
 cube1 <- spherical_roi(sp1, c(5,5,5), 3.5, fill=6)
 all(cube1 == 6)

 ## Create multiple spherical ROIs at once (preferred):
 centers <- rbind(c(5,5,5), c(3,3,3), c(7,7,7))
 vols <- spherical_roi_set(bvol = sp1,
                          centroids = centers, radius = 3.5, fill = 1)
 length(vols)  # 3

 ## Equivalent, less efficient lapply variant:
 vols2 <- lapply(seq_len(nrow(centers)), function(i) {
   spherical_roi(sp1, centers[i,], radius = 3.5, fill = 1)
 })

 # create an ROI centered around the real-valued coordinates: x=5, y=5, z=5
 vox <- coord_to_grid(sp1, c(5, 5, 5))
 cube <- spherical_roi(sp1, vox, 3.5)

neuroim2 documentation built on April 16, 2026, 5:07 p.m.