In neuroim there is basic support for creating regions of interest (ROI). To create a spherical ROI around a central point, we need an existing object of type BrainVolume or BrainSpace.
To create a spherical region of interest with a 5mm radius around a central voxel at i=20, j=20, k=20, we can do the following:
# attach MNI BrainSpace instance
data("MNI_SPACE_1MM")
# we create a spherical ROI centered around voxel coordinates [20,20,20] with a 5mm radius,
# filling all values in the ROI with 100.
sphere <- RegionSphere(MNI_SPACE_1MM, c(20,20,20), radius=5, fill=100)
# to extract the voxel coordinates of the sphere:
vox <- coords(sphere)
# to get the values at the coordinate locations
vals <- values(sphere)
all.equal(vals, rep(100, length(vals)))
#> [1] TRUE
To create a spherical ROI centered around an real coordinate in mm, we need to first convert the real-valued coordinate to a voxel-based coordinate. Suppose our real-world coordinate is at -50, -28, 10 in MNI space.
rpoint <- c(-50,-28,10)
# Because RegionSphere takes a coordinate in voxel units,
# we need to convert to the real-world MNI coordinate to grid coordinates.
vox <- coordToGrid(MNI_SPACE_1MM, rpoint)
sphere <- RegionSphere(MNI_SPACE_1MM, vox, radius=10, fill=1)
dim(coords(sphere))
#> [1] 4169 3
# convert back to MNI coordinates
mnicoords <- indexToCoord(MNI_SPACE_1MM, indices(sphere))
## compute center of mass of MNI coords in ROI (should be close to original coordinate)
centerOfMass <- colMeans(mnicoords)
centerOfMass
#> [1] -50.5 -27.5 10.5
We may want to convert a region of interest to a BrainVolume instance. But we don't want to store every value in dense grid. Here we can make use of the SparseBrainVolume class which only stores non-zero values.
sphere <- RegionSphere(MNI_SPACE_1MM, c(50,50,50), radius=10, fill=1)
sparsevol <- SparseBrainVolume(values(sphere),MNI_SPACE_1MM,indices=indices(sphere))
sum(sparsevol) == sum(values(sphere))
#> [1] TRUE
all(dim(sparsevol) == dim(MNI_SPACE_1MM))
#> [1] TRUE