These functions extract and replace medical image attributes that go beyond the core metadata associated with the NIfTI file formats.
imageAttributes(x)imageAttributes(x) <- value
A list of image attributes, or a modified object with these changed. These are essentially all attributes except those used for basic
niftiImage objects.
A niftiImage object.
A list of new image attributes to replace any existing ones.
Jon Clayden <code@clayden.org>
The DICOM (Digital Imaging and Communications in Medicine) format, and BIDS
(Brain Imaging Data Structure), which extends NIfTI, can both encapsulate
copious amounts of metadata about a scan and the patient. This metadata can
be useful for more advanced or research-focussed post-processing methods,
and standard R attributes are a natural place to store it. The
imageAttributes function returns a list of just these extended
attributes, if they exist, ignoring other attributes used by the package.
The replacement form allows this metadata to be modified or removed. These
functions currently only act on objects inheriting from the
niftiImage class.
More information about metadata captured by the BIDS format can be found at https://bids.neuroimaging.io or in the paper cited below.
K.J. Gorgolewski, T. Auer, V.D. Calhoun, et al. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments (2016). Scientific Data 3:160044. tools:::Rd_expr_doi("10.1038/sdata.2016.44").
The divest package can convert DICOM files to NIfTI formats,
and extract embedded metadata. More information about DICOM is available
at https://www.dicomstandard.org.
path <- system.file("extdata", "example.nii.gz", package="RNifti")
image <- readNifti(path)
imageAttributes(image)
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