RNifti (version 1.8.0)

readNifti: Read NIfTI or ANALYZE format files

Description

This function reads one or more NIfTI-1, NIfTI-2 or ANALYZE-7.5 files into R, using the standard NIfTI C library.

Usage

readNifti(file, internal = FALSE, volumes = NULL, json = c("ignore",
  "read", "convert"))

Value

An array or internal image, with class "niftiImage" (and possibly also "internalImage"), or a list of such objects if

file has length greater than one.

Arguments

file

A character vector of file names.

internal

Logical value. If FALSE (the default), an array of class "niftiImage", containing the image pixel or voxel values, will be returned. If TRUE, the return value will be an object of class "internalImage", which contains only minimal metadata about the image. Either way, the return value has an attribute which points to a C data structure containing the full image.

volumes

An integer vector giving the volumes to read (counting along all dimensions beyond the third jointly), or NULL, the default, in which case every volume is read. This cannot currently be set differently for each file read.

json

A string determining whether any BIDS-style JSON sidecar file is read in alongside the image(s). If "ignore", JSON files are ignored; if "read", they are read and attributes attached to the image using their names in the file; if "convert", element names are additionally converted to the down-cased naming convention of the tractor.base package. The jsonlite package is required for any reading of JSON.

Author

Jon Clayden <[e-mail]>

References

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

See Also

writeNifti

Examples

path <- system.file("extdata", "example.nii.gz", package="RNifti")
readNifti(path)
readNifti(path, internal=TRUE)