readDICOMFile: Read Single DICOM File
In oro.dicom: Rigorous - DICOM Input / Output

Description Usage Arguments Details Value Author(s) References See Also Examples

All information, both header and image, is read into a list structure from a DICOM file.

readDICOMFile(fname, boffset = NULL, endian = "little",
  flipud = TRUE, skipSequence = FALSE, pixelData = TRUE, warn = -1,
  debug = FALSE)

parseDICOMHeader(rawString, sq.txt = "", endian = "little",
  verbose = FALSE)

`fname`	is the file name of the DICOM image (with suffix).
`boffset`	is the number of bytes to skip at the beginning of the DICOM file (default = `NULL` which lets the code determine the starting point).
`endian`	is the endian-ness of the file (default is `"little"`).
`flipud`	is a logical variable for vertical flipping of the image (default is `TRUE`).
`skipSequence`	is a logical variable to skip all content contained in SequenceItem tags (default = `TRUE`).
`pixelData`	is a logical variable (default = `TRUE`) on whether or not the PixelData should be read from the DICOM files. This is useful when one wants to gather the DICOM header information without loading the images.
`warn`	is a number to regulate the display of warnings (default = -1). See `options` for more details.
`debug`	is a logical variable (default = `FALSE`) that regulates to display of intermediate processing steps.
`rawString`	is a vector of `raw` values taken directly from the DICOM file.
`sq.txt`	is an character string (default = “”) that indicates if the DICOM header field is embedded within a sequence.
`verbose`	is a logical variable (default = `FALSE`) that regulates to display of intermediate processing steps.

A while loop is used to traverse the unknown number of DICOM header fields contained in a single file. Information contained in “sequences” may be included/excluded according to the logical variable skipSequence (default = TRUE).

A resursive implementation of the code breaks the DICOM file into segments and calls itself to parse each segment.

Strict adherence to the DICOM standard is not required. Specifically, content is allowed to start at the first byte and the four characters ‘DICM’ are not required at bytes 129-132.

A list containing two elements:

hdr: all DICOM header fields (with or without “sequence” information).
img: the ‘image’ information.

Brandon Whitcher bwhitcher@gmail.com

Whitcher, B., V. J. Schmid and A. Thornton (2011). Working with the DICOM and NIfTI Data Standards in R, Journal of Statistical Software, 44 (6), 1–28. http://www.jstatsoft.org/v44/i06

Digital Imaging and Communications in Medicine (DICOM)
http://medical.nema.org
http://en.wikipedia.org/wiki/Digital_Imaging_and_Communications_in_Medicine

readDICOM

x <- readDICOMFile(system.file("dcm/Abdo.dcm", package="oro.dicom"))
graphics::image(t(x$img), col=grey(0:64/64), axes=FALSE, xlab="", ylab="",
                main="Abdo.dcm")

x <- readDICOMFile(system.file("dcm/Spine1.dcm", package="oro.dicom"))
graphics::image(t(x$img), col=grey(0:64/64), axes=FALSE, xlab="", ylab="",
                main="Spine1.dcm")