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

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

See Also

array, readDICOM, storage.mode

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"))

Convert Decimal to Base N Number in String

Description

This function converts the nonnegative integer to the specified base.

Usage

dec2base(n, base, len = 0)

dec2hex(n, len = 0)

Arguments

Details

This function converts the nonnegative integer n to the specified base, where n must be a nonnegative integer smaller than 2^52, base must be an integer between 2 and 36 and len suggests the length of the character string.

Value

The returned argument is a string.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

Examples

x <- dec2base(23, 2)

Lookup Tables for DICOM Header Information

Description

Lookup Tables for DICOM Header Information

Usage

data(dicom.dic)

Format

An object of class data.frame with 4188 rows and 5 columns.

Source

See references.

References

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

See Also

readDICOM, readDICOMFile.

Convert DICOM Header to Analyze

Description

A subset of header information from DICOM is placed into Analyze 7.5 format.

Usage

dicom2analyze(dcm, datatype = 4, reslice = TRUE, DIM = 3,
  descrip = "SeriesDescription", ...)

Arguments

Details

See the references.

Value

An object of class anlz.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

Analyze 7.5
http://rportal.mayo.edu/bir/ANALYZE75.pdf

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

See Also

convert.datatype.anlz, dicom2nifti, anlz

Examples

## Not run: 
dcmList <- dicomSeparate(system.file("hk-40", package="oro.dicom"))
require("oro.nifti")
dcmAnlz <- dicom2analyze(dcmList, datatype=4, mode="integer")
image(dcmAnlz)
orthographic(dcmAnlz)

## End(Not run)

Convert DICOM Header to NIfTI

Description

A subset of header information from DICOM is placed into NIfTI-1 format.

Usage

dicom2nifti(dcm, datatype = 4, units = c("mm", "sec"),
  rescale = FALSE, reslice = TRUE, qform = TRUE, sform = TRUE,
  DIM = 3, descrip = "SeriesDescription", aux.file = NULL, ...)

Arguments

Details

See the references.

Value

An object of class nifti.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

NIfTI-1
http://nifti.nimh.nih.gov/nifti-1

See Also

convert.datatype, dicom2analyze, nifti

Examples

## Not run: 
dcmList <- dicomSeparate(system.file("hk-40", package="oro.dicom"))
require("oro.nifti")
dcmNifti <- dicom2nifti(dcmList, datatype=4, mode="integer")
qform(dcmNifti)
sform(dcmNifti)
image(dcmNifti)
orthographic(dcmNifti)

## End(Not run)

Construct Data Frame from DICOM Headers

Description

A data frame is created given the valid DICOM fields provided by the user.

Usage

dicomTable(hdrs, stringsAsFactors = FALSE, collapse = "-",
  colSort = TRUE, verbose = FALSE, debug = FALSE)

Arguments

Value

Data frame where the rows correspond to images and the columns correspond to the UNION of all DICOM fields across all files in the list.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

Extract Single Field from DICOM Headers

Description

A particular DICOM field is extracted for a collection of DICOM headers.

Usage

extractHeader(hdrs, string, numeric = TRUE, names = FALSE,
  inSequence = TRUE)

Arguments

Details

The DICOM field is extracted from each DICOM header and placed into a vector.

Value

Vector of values from the requested DICOM field.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

readDICOM

Examples

x <- readDICOMFile(system.file("dcm/Abdo.dcm", package="oro.dicom"))
seriesDescription <- extractHeader(x$hdr, "SeriesDescription", numeric=FALSE)
IOP <- extractHeader(x$hdr, "ImageOrientationPatient", numeric=FALSE)

Convert Direction Cosines to Anatomical Direction

Description

For cross-sectional DICOM images the orientation must be derived from the Image Orientation (Patient) direction cosines.

Usage

getOrientation(xyz, delta = 0.0001)

Arguments

Details

C.7.6.2.1.1 Image Position And Image Orientation. The Image Position (0020,0032) specifies the x, y, and z coordinates of the upper left hand corner of the image; it is the center of the first voxel transmitted. Image Orientation (0020,0037) specifies the direction cosines of the first row and the first column with respect to the patient. These Attributes shall be provide as a pair. Row value for the x, y, and z axes respectively followed by the Column value for the x, y, and z axes respectively. The direction of the axes is defined fully by the patient's orientation. The x-axis is increasing to the left hand side of the patient. The y-axis is increasing to the posterior side of the patient. The z-axis is increasing toward the head of the patient. The patient based coordinate system is a right handed system; i.e., the vector cross product of a unit vector along the positive x-axis and a unit vector along the positive y-axis is equal to a unit vector along the positive z-axis.

Value

Anatomical direction shall be designated by the capital letters:

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

http://www.dclunie.com/medical-image-faq/html/part2.html

See Also

swapDimension

Converts DICOM Header Field to a Matrix

Description

Converts a vector of DICOM header information, assuming there are multiple entries per element of the vector, into a matrix.

Usage

header2matrix(hdr, ncol, sep = " ", byrow = TRUE)

Arguments

Value

Matrix with length(hdr) rows and ncol columns.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

extractHeader, matrix

Examples

x <- readDICOMFile(system.file("dcm/Abdo.dcm", package="oro.dicom"))
pixelSpacing <- extractHeader(x$hdr, "PixelSpacing", numeric=FALSE)
pSmat <- header2matrix(pixelSpacing, ncol=2)
IOP <- extractHeader(x$hdr, "ImageOrientationPatient", numeric=FALSE)
IOPmat <- header2matrix(IOP, ncol=6)

Match String to DICOM Header Field

Description

A convenient wrapper function that utilizes internal functions to match character strings with the DICOM header information.

Usage

matchHeader(hdr, string)

Arguments

Value

A logical vector of length length(hdr).

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

extractHeader

Examples

x <- readDICOMFile(system.file("dcm/Abdo.dcm", package="oro.dicom"))
modality <- extractHeader(x$hdr, "Modality", numeric=FALSE)
matchHeader(modality, "mr") # case insensitive by default

Check String Against DICOM Header Field to Produce Error Message or NEXT

Description

A function designed to break out of loops given information (or the lack thereof) contained in the DICOM header.

Usage

nextHeader(dcm, string, reference, str.warning, htmlfile = NULL,
  heading = 3, numeric = FALSE)

Arguments

Value

An expression to be evaluated and HTML content.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

extractHeader, matchHeader

Orthogonal Planes

Description

Functions to test the orientation for a single slice.

Usage

is.axial(imageOrientationPatient, axial = c("L", "R", "A", "P"))

is.coronal(imageOrientationPatient, coronal = c("L", "R", "H", "F"))

is.sagittal(imageOrientationPatient, sagittal = c("A", "P", "H", "F"))

Arguments

Value

Logical value.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

See Also

getOrientation

Examples

x <- readDICOMFile(system.file("dcm/Abdo.dcm", package="oro.dicom"))
iop <- header2matrix(extractHeader(x$hdr, "ImageOrientationPatient", FALSE), 6)
is.axial(iop)
is.coronal(iop)
is.sagittal(iop)

x <- readDICOMFile(system.file("dcm/Spine1.dcm", package="oro.dicom"))
iop <- header2matrix(extractHeader(x$hdr, "ImageOrientationPatient", FALSE), 6)
is.axial(iop)
is.coronal(iop)
is.sagittal(iop)

Parse DICOM Pixel or Spectroscopy Data

Description

These subroutines process the information contained after the DICOM header and process this information into an image (2D or 3D) or complex-valued vector.

Usage

parsePixelData(rawString, hdr, endian = "little", flipupdown = TRUE)

parseSpectroscopyData(rawString, hdr, endian = "little")

Arguments

Details

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

Value

A list containing two elements:

hdr

all DICOM header fields (with or without “sequence” information).

img

the ‘image’ information.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

Source

See references.

References

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

See Also

parseDICOMHeader, readDICOMFile.

Read All DICOM Files in a Directory

Description

All DICOM files are imported and a text file summarizing their content recorded.

Usage

readDICOM(path, recursive = TRUE, exclude = NULL, verbose = FALSE,
  counter, ...)

Arguments

Details

A for loop is used to process each DICOM file contained in the directory(ies). If only a single file is specified in the path, readDICOM will read that file only.

Value

A list structure with two major components:

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

readDICOMFile

Examples

## pixelData = TRUE
## The DICOM image data are read from readDICOM()

## Not run: 
dcmSphere <- readDICOM(system.file("sphere3", package="oro.dicom"), verbose=TRUE)

## End(Not run)

Read Single DICOM File

Description

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

Usage

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

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

Arguments

Details

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.

Value

A list containing two elements:

hdr

all DICOM header fields (with or without “sequence” information).

img

the ‘image’ information.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

readDICOM

Examples

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")

Convert DICOM Time/Date Entry

Description

The DICOM time entry (TM) is converted into two alternative formats: a text version of the original format and a number in seconds. The DICOM date entry (DA) is converted into a simple alternative format.

Usage

str2time(tt, format.out = "%02i:%02i:%08.5f")

str2date(dd, format.in = "%Y%m%d", format.out = "%d %b %Y")

Arguments

Details

DICOM “TM” format consists of a string of characters of the format hhmmss.frac; where hh contains hours (range “00” - “23”), mm contains minutes (range “00” - “59”), ss contains seconds (range “00” - “59”), and frac contains a fractional part of a second as small as 1 millionth of a second (range 000000 - 999999). A 24 hour clock is assumed. Midnight can be represented by only 0000 since 2400 would violate the hour range. The string may be padded with trailing spaces. Leading and embedded spaces are not allowed. One or more of the components mm, ss, or frac may be unspecified as long as every component to the right of an unspecified component is also unspecified. If frac is unspecified the preceding “.” may not be included. Frac shall be held to six decimal places or less to ensure its format conforms to the ANSI HISPP MSDS Time common data type. Examples:

1.

070907.0705 represents a time of 7 hours, 9 minutes and 7.0705 seconds.

2.

1010 represents a time of 10 hours, and 10 minutes.

3.

021 is an invalid value.

Notes: For reasons of backward compatibility with versions of this standard prior to V3.0, it is recommended that implementations also support a string of characters of the format hh:mm:ss.frac for this VR.

DICOM “DA” format A string of characters of the format yyyymmdd; where yyyy shall contain year, mm shall contain the month, and dd shall contain the day. This conforms to the ANSI HISPP MSDS Date common data type. Example:

1.

19930822 would represent August 22, 1993.

Notes: For reasons of backward compatibility with versions of this standard prior to V3.0, it is recommended that implementations also support a string of characters of the format yyyy.mm.dd for this VR.

Value

For “TM”, a list structure containing two fields

for “DA”, a simple character string.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

readDICOM

Examples

str2date("19930822")
str2time("112308")

Reslice Data Volume Using DICOM Header Fields

Description

The input data volume (assumed to be three-dimensional) is re-sliced so that each slice is in the axial plane. Orientation is preserved so that orthographic viewing is standardized.

Usage

swapDimension(img, dcm, digits = 2)

Arguments

Value

Multidimensional array with (potentially) permuted dimensions because of the reslicing operation. An additional attribute “pixdim” is provided in order to facilitate conversion from DICOM to NIFTI/ANALYZE.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

See Also

dicom2nifti, getOrientation

Write DICOM Table to ASCII File

Description

A wrapper to write.table specifically for DICOM tables.

Usage

writeHeader(dtable, filename, ...)

Arguments

Details

This function is a straightforward wrapper to write.table.

Value

None.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

References

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

See Also

write.table