oro.nifti (version 0.4.3)

readNIfTI: readNIfTI

Description

These functions read in the header information and multidimensional array from a binary file in NIfTI-1 format into a nifti-class object.

Usage

readNIfTI(fname, verbose=FALSE, warn=-1, reorient=TRUE, call=NULL)

Arguments

fname

is the file name of the NIfTI file(s).

verbose

is a logical variable (default = FALSE) that allows text-based feedback during execution of the function.

warn

is a number to regulate the display of warnings (default = -1). See options for more details.

reorient

is a logical variable (default = TRUE) that enforces Qform/Sform transformations.

call

keeps track of the current function call for use in the NIfTI extension.

Value

• An object of class nifti.

Details

The readNIfTI function utilizes internal methods readBin and readChar to efficiently extract information from the binary file(s).

Current acceptable data types include [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

References

NIfTI-1 http://nifti.nimh.nih.gov/

See Also

readAFNI, readANALYZE

Examples

url <- "http://nifti.nimh.nih.gov/nifti-1/data/filtered_func_data.nii.gz"
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "filtered_func_data")
download.file(url, urlfile, quiet=TRUE)
## The NIfTI file provided here contains the first 18 volumes (10\%)
## of the original data set
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "filtered_func_data")
(ffd <- readNIfTI(urlfile))
image(ffd, oma=rep(2,4))
orthographic(ffd, oma=rep(2,4))
## 27 scans of Colin Holmes (MNI) brain co-registered and averaged
## NIfTI two-file format
URL <- "http://imaging.mrc-cbu.cam.ac.uk/downloads/Colin/colin_1mm.tgz"
urlfile <- file.path(tempdir(), "colin_1mm.tgz")
download.file(URL, dest=urlfile, quiet=TRUE)
untar(urlfile, exdir=tempdir())
colin <- readNIfTI(file.path(tempdir(), "colin_1mm"))
image(colin, oma=rep(2,4))
orthographic(colin, oma=rep(2,4))