freesurferformats (version 1.1.0)

write.nifti1: Write header and data to a file in NIFTI v1 format.

Description

Write header and data to a file in NIFTI v1 format.

Usage

write.nifti1(filepath, niidata, niiheader = NULL, ...)

Value

invisible named list with the entries header (the header that was written) and data (the data that was written, or NULL if no data was passed).

Arguments

filepath

the file to write. The extension should be '.nii' or '.nii.gz' for a single file NIFTI image, and '.hdr', '.img' (optionally followed by '.gz') for a NIFTI v1 pair, i.e. a header file with the voxel data in a separate '.img' file. Which of the two is written follows from the magic field of the header: 'n+1' means a single file, 'ni1' means a pair. See ni1header.template.

niidata

array of numeric or integer data, with up to 7 dimensions. Will be written to the file with the datatype and bitpix specified in the 'niiheader' argument. Set to NULL and pass a 'niiheader' to write only the header, and remember to adapt 'magic' in the header.

niiheader

an optional NIFTI v1 header that is suitable for the passed 'niidata'. If not given, one will be generated with ni1header.for.data.

...

additional parameters passed to ni1header.for.data. Only used if 'niiheader' is NULL.

See Also

Other nifti1 writers: nii1header.for.mgh(), write.fs.morph.ni1()

Examples

# A single file NIFTI image (the default):
data <- array(1:24, dim = c(4, 3, 2))
nii_file <- tempfile(fileext = ".nii")
write.nifti1(nii_file, data)

# A NIFTI v1 pair, i.e. a header plus a separate data file. Ask for a pair
# header by passing 'pair = TRUE' (this is passed on to the header generator):
write.nifti1(tempfile(fileext = ".hdr"), data, pair = TRUE)

# The NIFTI v1 pair files can be read back with the volume reader:
hdr_file <- tempfile(fileext = ".hdr")
write.nifti1(hdr_file, data, pair = TRUE)
vol <- read.fs.volume(hdr_file, with_header = TRUE)
print(dim(vol$data))