tractor.base (version 1.1.0)

newMriImageFromFile: Working with MRI images stored in NIfTI and Analyze formats

Description

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

Usage

newMriImageFromFile(fileName, fileType = NULL)
newMriImageMetadataFromFile(fileName, fileType = NULL)
writeMriImageToFile(image, fileName = NULL, fileType = NA, datatype = NULL, overwrite = TRUE)
identifyImageFileNames(fileName, fileType = NULL, errorIfMissing = TRUE)
imageFileExists(fileName, fileType = NULL)
removeImageFilesWithName(fileName)

Arguments

fileName

A file name, with or without appropriate extension.

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.

datatype

A storage data type. See getDataTypeByNiftiCode.

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.

errorIfMissing

Logical value: raise an error if no suitable files were found?

Value

• newMriImageFromFile and newMriImageMetadataFromFile return the appropriate image or metadata object. imageFileExists returns TRUE if an existing file with the specified name exists (all file extensions are checked), and FALSE otherwise. removeImageFilesWithName returns the result of unlink() applied to all relevant files. writeMriImageToFile and identifyImageFileNames return a list with the following elements, describing the identified or written files:
• fileStem
  The file name without extension.
• headerFile
  The full header file name.
• imageFile
  The full image file name.
• format
  The format of the files ("Nifti" or "Analyze"). Not returned by writeMriImageToFile.

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. 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 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) are ANALYZE, NIFTI, NIFTI_PAIR (the two-file NIfTI format), ANALYZE_GZ, NIFTI_GZ and NIFTI_PAIR_GZ. The latter three are gzipped versions of the former three. NIFTI_GZ is recommended unless there is a need for one of the others. This 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.

See Also

The NIfTI-1 standard (http://nifti.nimh.nih.gov/nifti-1), MriImage, MriImageMetadata, getDataTypeByNiftiCode and unlink.