gifti_xml: Get GIFTI XML representation of data.

In freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats

Description

Creates a GIFTI XML tree from your datasets (vectors and matrices). The tree can be further modified to add additional data, or written to a file as is to produce a valid GIFTI file (see gifti_xml_write).

Usage

gifti_xml(
  data_array,
  intent = "NIFTI_INTENT_SHAPE",
  datatype = "NIFTI_TYPE_FLOAT32",
  encoding = "GZipBase64Binary",
  endian = "LittleEndian",
  transform_matrix = NULL,
  force = FALSE
)

Arguments

data_array	list of data vectors and/or data matrices.
intent	vector of NIFTI intent strings for the data vectors in 'data_array' parameter, see convert_intent. Example: 'NIFTI_INTENT_SHAPE'. See https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/group__NIFTI1__INTENT__CODES.html.
datatype	vector of NIFTI datatype strings. Example: 'NIFTI_TYPE_FLOAT32'. Should be suitable for your data.
encoding	vector of encoding definition strings. One of 'ASCII', 'Base64Binary', 'GZipBase64Binary'.
endian	vector of endian definition strings. One of 'LittleEndian' or 'BigEndian'. See convert_endian.
transform_matrix	optional, a list of transformation matrices, one for each data_array. If one of the data arrays has none, pass ‘NA'. Each transformation matrix in the outer list has to be a 4x4 matrix or given as a named list with entries ’transform_matrix', 'data_space', and 'transformed_space'. Here is an example: list('transform_matrix'=diag(4), 'data_space'='NIFTI_XFORM_UNKNOWN', 'transformed_space'='NIFTI_XFORM_UNKNOWN').
force	logical, whether to force writing the data, even if issues like a mismatch of datatype and data values are detected.

Value

xml tree, see xml2 package. One could modify this tree as needed using xml2 functions, e.g., add metadata.

Note

Unless you want to modify the returned tree manually, you should not need to call this function. Use gifti_writer instead.

References

See https://www.nitrc.org/frs/download.php/2871/GIFTI_Surface_Format.pdf

See Also

The example for gifti_xml_write shows how to modify the tree.

Examples

## Not run: 
  my_data_sets = list(rep(3.1, 3L), matrix(seq(6)+0.1, nrow=2L));
  transforms = list(NA, list('transform_matrix'=diag(4), 'data_space'='NIFTI_XFORM_UNKNOWN',
   'transformed_space'='NIFTI_XFORM_UNKNOWN'));
  xmltree = gifti_xml(my_data_sets, datatype='NIFTI_TYPE_FLOAT32', transform_matrix=transforms);
  # Verify that the tree is a valid GIFTI file:
  gifti_xsd = "https://www.nitrc.org/frs/download.php/158/gifti.xsd";
  xml2::xml_validate(xmltree, xml2::read_xml(gifti_xsd));

## End(Not run)

freesurferformats documentation built on Feb. 11, 2022, 5:06 p.m.