Working with Image Volumes

In neuroim2: Data Structures for Brain Imaging Data

knitr::opts_chunk$set(collapse = T, comment = "#>")

Reading a NIFTI formatted image volume

The way to read an volumetric image file is to use read_vol:

    library(neuroim2)
    file_name <- system.file("extdata", "global_mask2.nii.gz", package="neuroim2")
    vol <- read_vol(file_name)

Working with image volumes

Information about the geometry of the image volume is shown here:

    print(vol)

read_vol returns an object of class NeuroVol object which extends an R array and has 3 dimensions (x,y,z).

    class(vol)

    is.array(vol)

    dim(vol)

    vol[1,1,1]

    vol[64,64,24]

Arithmetic can be performed on images as if they were ordinary arrays:

    vol2 <- vol + vol
    sum(vol2) == 2 * sum(vol)

    vol3 <- vol2 - 2*vol
    all(vol3 == 0)

A numeric image volume can be converted to a binary image as follows:

    vol2 <- as.logical(vol)
    class(vol2)
    print(vol2[1,1,1])

We can also create a NeuroVol instance from an array or numeric vector. First we consruct a standard R array:

    x <- array(0, c(64,64,64))

Now we reate a NeuroSpace instance that describes the geometry of the image including, at minimum, its dimensions and voxel spacing.

    bspace <- NeuroSpace(dim=c(64,64,64), spacing=c(1,1,1))
    vol <- NeuroVol(x, bspace)
    vol

We do not usually have to create NeuroSpace objects, because geometric information about an image is automatically determined from information stored in the image file header. Thus, NeuroSpace objects are usually copied from existing images using the space extractor function when needed:

    vol2 <- NeuroVol((vol+1)*25, space(vol))
    max(vol2)
    space(vol2)

Writing a NIFTI formatted image volume

When we're ready to write an image volume to disk, we use write_vol

    write_vol(vol2, "output.nii")

    ## adding a '.gz' extension results ina gzipped file.
    write_vol(vol2, "output.nii.gz")

neuroim2 documentation built on April 11, 2025, 5:46 p.m.