oro.nifti (version 0.1.4)

writeNIfTI: writeNIfTI

Description

This function saves a NIfTI-class object to a single binary file in NIfTI format.

Usage

writeNIfTI(nim, filename, gzipped = TRUE, verbose = FALSE, warn = -1)

Arguments

nim

is an object of class nifti.

filename

is the path and file name to save the NIfTI file (.nii) without the suffix.

gzipped

is a character string that enables exportation of compressed (.gz) files (default = TRUE).

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.

Value

• Nothing.

Details

The writeNIfTI function utilizes the internal writeBin and writeChar command to write information to a binary file.

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

References

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

See Also

writeANALYZE

Examples

norm <- dnorm(seq(-5, 5, length=32), sd=2)
norm <- (norm-min(norm)) / max(norm-min(norm))
img <- outer(outer(norm, norm), norm)
img <- round(255 * img)
img[17:32,,] <- 255 - img[17:32,,]
img.nifti <- nifti(img) # create NIfTI object

writeNIfTI(img.nifti, "test-nifti-image-uint8", verbose=TRUE)
## These files should be viewable in, for example, FSLview
## Make sure you adjust the min/max values for proper visualization
data <- readNIfTI("test-nifti-image-uint8", verbose=TRUE)
image(img.nifti, oma=rep(2,4), bg="white")
image(data, oma=rep(2,4), bg="white")
abs.err <- abs(data - img.nifti)
image(as(abs.err, "nifti"), zlim=range(img.nifti), oma=rep(2,4), bg="white")

## Loop through all possible data types
datatypes <- list(code=c(2, 4, 8, 16, 64),
                  name=c("uint8", "int16", "int32", "float", "double"))
equal <- vector("list")
for (i in 1:length(datatypes$code)) {
  fname <- paste("test-nifti-image-", datatypes$name[i], sep="")
  rm(img.nifti)
  img.nifti <- nifti(img, datatype=datatypes$code[i])
  writeNIfTI(img.nifti, fname, verbose=TRUE)
  equal[[i]] <- all(readNIfTI(fname) == img)
}
names(equal) <- datatypes$name
unlist(equal)