writeNifti {RNifti}

Write a NIfTI or ANALYZE format file

Description

These functions write an image to NIfTI-1, NIfTI-2 or ANALYZE-7.5 format, using the standard NIfTI C library.

Usage

writeNifti(image, file, template = NULL, datatype = "auto", version = 1,
  compression = 6)

writeAnalyze(image, file, template = NULL, datatype = "auto",
  compression = 6)

Arguments

image

An image, in any acceptable form (see asNifti).

file

A character string containing a file name. If this has no file extension suffix, or ends with "nii", the single-file NIfTI format is used; if the suffix is "nii.gz", the compressed single-file format is used; if the suffix is "hdr" or "img", the NIfTI pair two-file format is used; if it's "hdr.gz" or "img.gz", the compressed pair format is used. If any other extension is present it will be ignored, and ".nii" appended.

template

An optional template object to derive NIfTI properties from. Passed to asNifti if image is an array.

datatype

The NIfTI datatype to use when writing the data out. The default, "auto" uses the R type or, for internal images, the original datatype. Other possibilities are "float", "int16", etc., which may be preferred to reduce file size. However, no checks are done to ensure that the coercion maintains precision.

version

An integer (1 or 2) giving the NIfTI file format version to use. Version 2 is usually only needed for very large images or where metadata needs to be stored with high precision. The types available for storing the pixel data are the same in both cases.

compression

The gzip compression level to use, an integer between 0 (none) and 9 (maximum). Ignored if an uncompressed format is implied by the requested file name.

Value

An invisible, named character vector giving the image and header file names written to.

Note

The ANALYZE-7.5 file format is a legacy format and use of it is not recommended, except for compatibility. In particular, the format does not reliably specify the spatial orientation of the image.

Author(s)

Jon Clayden <[e-mail]>

References

The NIfTI-1 standard (https://www.nitrc.org/docman/view.php/26/64/nifti1.h).

See Also

readNifti, asNifti

Examples

## Not run: writeNifti(im, "image.nii.gz", datatype="float")