# Simple Image Input/Output

    library(neurobase)

# The nifti object

Note: Throughout this post, I will refer to an image on hard disk as a NIfTI, which is a file that generally has the extension “.nii” or “.nii.gz”. I will refer to the object in R as a `nifti` (note the change of font and case).

In this tutorial we will discuss the basics of reading the `nifti` object in R. There are many objects in R that represent imaging data. The Neuroconductor project chose the `nifti` object from the `oro.nifti` package as one of the the basic building blocks because it has been widely used in other packages, has been tested over a period of time, and inherits the properties of an `array` in R.

# Downloading an Image

Let’s say you have a T1-weighted NIfTI on your machine. If you do not, we can download one. We are downloading this to a temporary file since we don’t need it after the session is over:

    t1_file = tempfile(fileext = ".nii.gz")
    url = paste0("https://johnmuschelli.com/",
                           "open_ms_data/", "cross_sectional/",
                           "raw/patient01/T1W.nii.gz")
    download.file(url, destfile = t1_file)
    t1_file
    #> [1] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//Rtmpq8CrQ4/fileef5e5b48fb90.nii.gz"

# Reading in an image

Here we will use the `readnii` function to read in the image to an object called `img`:

    library(neurobase)
    img = readnii(t1_file)
    img
    #> NIfTI-1 format
    #>   Type            : nifti
    #>   Data Type       : 4 (INT16)
    #>   Bits per Pixel  : 16
    #>   Slice Code      : 0 (Unknown)
    #>   Intent Code     : 0 (None)
    #>   Qform Code      : 2 (Aligned_Anat)
    #>   Sform Code      : 1 (Scanner_Anat)
    #>   Dimension       : 408 x 512 x 152
    #>   Pixel Dimension : 0.43 x 0.43 x 0.82
    #>   Voxel Units     : mm
    #>   Time Units      : Unknown

We see the output is a `nifti` object. We can think of this as an array with additional information (called a header). We can do simple operations on the image, such as `sum`:

    sum(img)
    #> [1] 4073996312
    sum(img > 1000)
    #> [1] 278650

# Writing Images

Let’s say we want to set all values greater than 1000 to 1000 and then write the image out. We will use the `writenii` function. We will copy `img` to `img2` because we want to keep `img` as is. Again we will write the image to a temporary file because we don’t need this after the session:

    img2 = img
    img2[ img2 > 1000] = 1000
    outfile = tempfile(fileext = ".nii.gz")
    writenii(img2, outfile)
    file.exists(outfile)
    #> [1] TRUE

# Operations of `nifti` objects

Although the `nifti` object is not a standard R object, you can perform standard operations on these objects, such as addition/subtraction and logic. This is referred to “overloaded” operators.

## Logical operators

For example, if we want to create a `nifti` object with binary values, where the values are `TRUE` if the values in `img` are greater than 0, we can simply write:

    above_zero = img > 0
    class(above_zero)
    #> [1] "nifti"
    #> attr(,"package")
    #> [1] "oro.nifti"
    img_data(above_zero)[1]
    #> [1] FALSE

We will refer to binary images/`nifti` objects as “masks”.

We can combine multiple operators, such as creating a binary mask for value greater than 0 and less than 2.

    class(img > 0 & img < 2)
    #> [1] "nifti"
    #> attr(,"package")
    #> [1] "oro.nifti"

## Arithmetic on `nifti` objects

We can also show the

    class(img * 2)
    #> [1] "nifti"
    #> attr(,"package")
    #> [1] "oro.nifti"
    class(img + (img / 4))
    #> [1] "nifti"
    #> attr(,"package")
    #> [1] "oro.nifti"
    class(img * img)
    #> [1] "nifti"
    #> attr(,"package")
    #> [1] "oro.nifti"
    class(img^2)
    #> [1] "nifti"
    #> attr(,"package")
    #> [1] "oro.nifti"

# Visualization of `nifti` objects

## Orthographic view

The `neurobase::ortho2` function expands the `oro.nifti::orthographic` function for displaying `nifti` objects in 3 different planes:

    neurobase::ortho2(img)

We see that in `ortho2` there are annotations of the orientation of the image. Again, if the image was not reoriented, then these many not be correct. You can turn these off with the `add.orient` argument:

    neurobase::ortho2(img, add.orient = FALSE)

## Single slice view

We may want to view a single slice of an image. The `oro.nifti::slice` function can be used here.

    oro.nifti::slice(img, z = 45)

We can also get a view of multiple slices:

    oro.nifti::slice(img, z = c(45, 50))

### Different Planes

We can specify `z` the same way but change the `plane` to be different to get a different slice of the brain:

    oro.nifti::slice(img, z = 52, plane = "sagittal")

We can similarly do the same for “coronal” slices.

## Overlaying slices

We can also overlay one slice of an image upon another using the `oro.nifti::overlay` function. Here we must specify `plot.type` for only one slice.

    overlay(img, y = img > quantile(img, 0.9), z = 45, plot.type = "single",
            NA.y = TRUE)