The easiest way to read an image file is to use loadVolume:
fileName <- system.file("extdata", "global_mask.nii", package="neuroim")
vol <- loadVolume(fileName)
Information about the geometry of the image volume is easily accessed:
print(vol)
#> BrainVolume
#> Type : DenseBrainVolume
#> Dimension : 64 64 25
#> Spacing : 3.5 X 3.5 X 3.70000004768372
#> Origin : 110 X -110 X -46.25
#> Axes : Right-to-Left Posterior-to-Anterior Inferior-to-Superior
loadVolume returns an object of class DenseBrainVolume which extends an R array' and has 3 dimensions (x,y,z).
class(vol)
#> [1] "DenseBrainVolume"
#> attr(,"package")
#> [1] "neuroim"
is.array(vol)
#> [1] TRUE
dim(vol)
#> [1] 64 64 25
vol[1,1,1]
#> [1] 0
vol[64,64,24]
#> [1] 0
Arithmetic can be performed on images as if they were ordinary arrays:
vol2 <- vol + vol
sum(vol2) == 2 * sum(vol)
#> [1] TRUE
vol3 <- vol2 - 2*vol
all(vol3 == 0)
#> [1] TRUE
A numeric image volume can be converted to a binary image as follows:
vol2 <- as.logical(vol)
print(vol2[1,1,1])
#> [1] FALSE
We can also create a BrainVolume instance from an array or numeric vector:
# create an 64X64X64 array of zeros
x <- array(0, c(64,64,64))
# create a 'BrainSpace' instance that describes the geometry of the image including, at minimu its dimensions and voxel spacing
bspace <- BrainSpace(Dim=c(64,64,64), spacing=c(1,1,1))
vol <- BrainVolume(x, bspace)
vol
#> BrainVolume
#> Type : DenseBrainVolume
#> Dimension : 64 64 64
#> Spacing : 1 X 1 X 1
#> Origin : 0 X 0 X 0
#> Axes : Left-to-Right Posterior-to-Anterior Inferior-to-Superior
We do not usually have to create BrainSpace objects because this information is usually read from disk. Thus, BrainSpace objects are usually copied from existing images using the space extractor function when needed:
vol2 <- BrainVolume((vol+1)*25, space(vol))
max(vol2)
#> [1] 25
space(vol2)
#> BrainSpace
#> Type : BrainSpace
#> Dimension : 64 64 64
#> Spacing : 1 X 1 X 1
#> Origin : 0 X 0 X 0
#> Coordinate Transform : 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1
When we're ready to write an image volume to disk, we use writeVolume
writeVolume(vol2, "output.nii")
## adding a '.gz' extension results ina gzipped file.
writeVolume(vol2, "output.nii.gz")