readNIfTI

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

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

nifti_header(fname, verbose = FALSE, warn = -1)

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.
read_data	Should the data be read in? If this is FALSE, then an array of NAs are given instead of the true data. Useful if you are simply interested in the header.
rescale_data	Should the data be rescaled using the slope and intercept values? If so, slope and intercept will be reset

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

list("UINT8")

BINARY (1 bit per voxel)

list("INT16")

SIGNED SHORT (16 bits per voxel)

list("INT32")

SINGED INT (32 bits per voxel)

list("FLOAT32")

FLOAT (32 bits per voxel)

list("DOUBLE64")

DOUBLE (64 bits per voxel)

list("UINT16")

UNSIGNED SHORT (16 bits per voxel)

list("UINT32")

UNSIGNED INT (32 bits per voxel)

References

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

See also

readAFNI, readANALYZE

Author

Brandon Whitcher bwhitcher@gmail.com,
Volker Schmid volkerschmid@users.sourceforge.net,
Andrew Thornton zeripath@users.sourceforge.net

Examples

if (FALSE) {
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))
#> NIfTI-1 format
#>   Type            : niftiExtension
#>   Data Type       : 4 (INT16)
#>   Bits per Pixel  : 16
#>   Slice Code      : 0 (Unknown)
#>   Intent Code     : 0 (None)
#>   Qform Code      : 0 (Unknown)
#>   Sform Code      : 0 (Unknown)
#>   Dimension       : 64 x 64 x 21 x 64
#>   Pixel Dimension : 1 x 1 x 1 x 1
#>   Voxel Units     : Unknown
#>   Time Units      : Unknown
image(ffd, oma=rep(2,4))

orthographic(ffd, oma=rep(2,4))

if (FALSE) {
## 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))
}