Create Arrays from DICOM Headers/Images

A DICOM list structure is used to produce a multi-dimensional array representing a single acquisition of medical imaging data.

create3D(dcm, mode = "integer", transpose = TRUE, pixelData = TRUE,
  mosaic = FALSE, mosaicXY = NULL, sequence = FALSE,
  boffset = NULL)

create4D(dcm, mode = "integer", transpose = TRUE, pixelData = TRUE,
  mosaic = FALSE, mosaicXY = NULL, nslices = NULL, ntimes = NULL,
  instance = TRUE, sequence = FALSE)

Arguments

dcm	is the DICOM list structure (if pixelData = TRUE) or the DICOM header information (if pixelData = FALSE).
mode	is a valid character string for storage.mode.
transpose	is available in order to switch the definition of rows and columns from DICOM (default = TRUE.
pixelData	is a logical variable (default = TRUE) that is associated with the DICOM image data being pre-loaded.
mosaic	is a logical variable (default = FALSE) to denote storage of the data in Siemens ‘Mosaic’ format.
mosaicXY	is a vector of length two that provides the (x,y) dimensions of the individual images. Default behavior is to use the AcquisitonMatrix to determine the (x,y) values.
sequence	is a logical variable (default = FALSE) on whether to look in SequenceItem entries for DICOM header information.
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).
nslices	is the third dimension of the array. Attempts are made to determine this number from the DICOM data.
ntimes	is the fourth dimension of the array. Attempts are made to determine this number from the DICOM data.
instance	is a logical variable (default = TRUE) that determines whether or not to access the InstanceNumber field in the DICOM header to help order the slices.

Value

Multi-dimensional array of medical imaging data.

References

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

See also

array, readDICOM, storage.mode

Author

Brandon Whitcher bwhitcher@gmail.com

Examples

load(system.file("hk-40/hk40.RData", package="oro.dicom"))
dcmList <- hk40
dcmImage <- create3D(dcmList)
image(dcmImage[,,1], col=grey(0:64/64), axes=FALSE, xlab="", ylab="",
      main=paste("First Slice from HK-40"))

imagePositionPatient <- attributes(dcmImage)$ipp
dSL <- abs(diff(imagePositionPatient[,3]))
plot(dSL, ylim=range(range(dSL) * 1.5, 0, 10), xlab="Image", ylab="mm",
     main="Difference in Slice Location")


if (FALSE) {
## pixelData = FALSE
## The DICOM image data are read from create3D()
## This may save on memory for large batches of DICOM data
dcmList <- readDICOM(system.file("hk-40", package="oro.dicom"),
                     pixelData=FALSE)
dcmImage <- create3D(dcmList, pixelData=FALSE)
image(dcmImage[,,1], col=grey(0:64/64), axes=FALSE, xlab="", ylab="",
      main=paste("First Slice from HK-40 (again)"))
}
## mosaic = TRUE
mosaicFile <- system.file("dcm/MR-sonata-3D-as-Tile.dcm", package="oro.dicom")
dcm <- readDICOMFile(mosaicFile)
image(t(dcm$img), col=grey(0:64/64), axes=FALSE, xlab="", ylab="",
      main="Siemens MOSAIC")

dcmImage <- create3D(dcm, mode="integer", mosaic=TRUE)
z <- trunc(dim(dcmImage)[3]/2)
image(dcmImage[,,z], col=grey(0:64/64), axes=FALSE, xlab="", ylab="",
      main=paste("Slice", z, "from Siemens MOSAIC"))