Read ANALYZE 7.5 header from file.

Read the header of an ANALYZE 7.5 file, i.e. of a file in the two-file format that stores the voxel data in a separate .img file.

Usage

read.analyze.header(filepath)

Arguments

filepath

character string, the path to the .hdr file. The base name without the extension is accepted as well, see analyze.pair.files.

Value

named list with the ANALYZE 7.5 header fields, in the field naming of the format specification. See analyzeheader.template for a description of all of them. In addition to the fields of the specification, the following entries are present:

endian

character string, the endianness of the file, 'little' or 'big'. It is detected from the sizeof_hdr field.

magic

character string, the 4 bytes at offset 344 (which are the smin field of the ANALYZE specification), interpreted as a string. It is empty for ANALYZE files, see is.analyze.file.

header_format

character string, always 'analyze' here. The other variant of the two-file format is reported as 'nifti1_pair', see read.fs.volume.analyze.

spm_origin

integer vector of length 3, the interpretation that SPM gives to the originator field: the voxel coordinates of the image origin, as stored in the first 6 bytes of the field. It is NULL if all of them are zero, which means that the field does not store an origin.

originator_bytes

raw vector of length 10, the unmodified content of the originator field. The originator entry is the same content with the zero bytes removed and interpreted as a string, which loses information for the files in which SPM stores the image origin there.

filepath_header, filepath_image

character strings, the paths of the two files of the pair.

Note

ANALYZE 7.5 does not define the meaning of the world coordinate system of an image: the header stores the voxel sizes but neither the direction of the voxel axes nor the position of the image in space. This function therefore reports the fields as they are stored and does not derive a transformation matrix. See read.fs.volume.analyze for the ways to get a matrix anyway, and for what is known and unknown about them.

See also

read.analyze.data, analyzeheader.template

Examples

hdrfile <- system.file("extdata", "analyze", "tiny_u8.hdr",
  package = "freesurferformats", mustWork = TRUE
)
analyzeheader <- read.analyze.header(hdrfile)
analyzeheader$datatype
#> [1] 2
analyzeheader$pix_dim
#> [1] 1 1 2 3 1 1 1 1