oro.dicom: create3D – R documentation

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create3D

Create Arrays from DICOM Headers/Images

Description

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

Usage

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.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

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")

## Not run: 
## 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)"))

## End(Not run)
## 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"))

oro.dicom

Rigorous - DICOM Input / Output

v0.5.3

BSD_3_clause + file LICENSE

Authors

Brandon Whitcher [aut, cre]

Initial release

2019-10-25