readImageFile: Reading and writing image files

Description

Functions for reading, writing, locating, copying and removing MRI images stored in NIfTI, Analyze, MGH and MRtrix formats.

Usage

readImageFile(fileName, metadataOnly = FALSE, volumes = NULL,
  sparse = FALSE, mask = NULL, reorder = TRUE, ...)
writeImageFile(image, fileName = NULL,
  fileType = getOption("tractorFileType"), overwrite = TRUE,
  datatype = "fit", writeTags = FALSE)

Value

readImageFile returns an MriImage

object. writeImageFile returns a list giving details of the file paths that were written to.

Arguments

fileName: A file path, with or without appropriate extension.
metadataOnly: Logical value: if TRUE, only metadata are read into the object.
volumes: An optional integer vector specifying a subset of volumes to read (generally to save memory). If given, only the requested volumes in the 4D file will be read.
sparse: Logical value: should the image data be stored in a SparseArray object?
mask: An optional MriImage object representing a mask, outside of which the image to be read should be considered to be zero. This can be used to save memory when only a small part of a large image is of interest. Ignored if sparse is not TRUE.
reorder: Logical value: should the image data be reordered to LAS? This is recommended in most circumstances.
...: Additional arguments to identifyImageFileNames.
image: An MriImage object.
fileType: A character vector of length one, giving the file type required or expected. If this option is missing, the file type used for writing images will be taken from the tractorFileType option. See Details.
overwrite: Logical value: overwrite an existing image file? An error will be raised if there is an existing file and this is set to FALSE.
datatype: A datatype string, such as "uint8" or "float", specifying the pixel datatype to use when storing the data. If specified, this must be a type supported by the requested (or default) file format. The default, "fit", results in a datatype being chosen that is wide enough to fit the range of the data elements. An error will arise if there's no such type.
writeTags: Logical value: should tags be written in YAML format to an auxiliary file?

Author

Jon Clayden

Details

NIfTI and Analyze are related formats for storing magnetic resonance images. NIfTI is a more recent extension of Analyze, and contains more specific information about, for example, the orientation of the image. Its use is therefore recommended where possible. MGH format is used by the popular image processing package FreeSurfer, and MRtrix format by the software of the same name. These formats use a number of different file extensions, but the details are abstracted away from the user by these functions.

TractoR does not allow for files with the same basic name using multiple Analyze/NIfTI/MGH/MRtrix formats in a single directory (e.g. "foo.nii" AND "foo.img"), and these functions will produce an error if multiple compatible files exist.

Suitable values for fileType (and the tractorFileType option, which is used as a default for writing) are "NIFTI", "NIFTI_PAIR" (the two-file NIfTI format), "MGH", and corresponding gzipped versions of these with "_GZ" appended. File types "ANALYZE" and "MRTRIX", and "_GZ" variants, are additionally available for reading only. "NIFTI_GZ" is the default value for the tractorFileType option, but that can be changed using a call to options, or by setting the TRACTOR_FILETYPE environment variable before loading the tractor.base package.

References

Please cite the following reference when using TractoR in your work:

J.D. Clayden, S. Muñoz Maniega, A.J. Storkey, M.D. King, M.E. Bastin & C.A. Clark (2011). TractoR: Magnetic resonance imaging and tractography with R. Journal of Statistical Software 44(8):1-18. tools:::Rd_expr_doi("10.18637/jss.v044.i08").