readNIfTI {oro.nifti} | R Documentation |
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,
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 = |
warn |
is a number to regulate the display of warnings (default = -1).
See |
reorient |
is a logical variable (default = |
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 |
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)
Value
An object of class nifti
.
Author(s)
Brandon Whitcher bwhitcher@gmail.com,
Volker Schmid
volkerschmid@users.sourceforge.net,
Andrew Thornton
zeripath@users.sourceforge.net
References
NIfTI-1
http://nifti.nimh.nih.gov/
See Also
Examples
## Not run:
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)
## End(Not run)
## 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))
## Not run:
## 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))
## End(Not run)