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tractor.base (version 2.3.0)

newMriImageFromDicom: Functions for reading images from DICOM files

Description

Functions for reading images from DICOM files.

Usage

newMriImageFromDicom(fileName, untileMosaics = TRUE)
newMriImageFromDicomDirectory(dicomDir, readDiffusionParams = FALSE, untileMosaics = TRUE)
newMriImageFromDicomMetadata(metadata, flipY = TRUE, untileMosaics = TRUE)
newMriImageMetadataFromDicom(fileName, untileMosaics = TRUE)
newMriImageMetadataFromDicomMetadata(dicom, untileMosaics = TRUE)

Arguments

fileName
Character vector of length one giving the name of a DICOM file.
untileMosaics
Logical value: should Siemens mosaic images be converted into 3D volumes? This may occasionally be performed in error, which can be prevented by setting this value to FALSE.
dicomDir
Character vector of length one giving the name of a directory containing DICOM files.
readDiffusionParams
Logical value: should diffusion MRI parameters (b-values and gradient directions) be retrieved from the files if possible?
metadata, dicom
DicomMetadata objects.
flipY
Logical value: should the image be flipped in the Y direction? Usually this is appropriate to convert between DICOM's LPS and TractoR's LAS storage conventions.

Value

  • newMriImageFromDicom and newMriImageFromDicomMetadata return an MriImage object. newMriImageMetadataFromDicom and newMriImageMetadataFromDicomMetadata return an MriImageMetadata object. newMriImageFromDicomDirectory returns a list containing elements
  • imageAn MriImage object.
  • bValuesDiffusion b-values, if requested. Will be NA if the information could not be found in the files.
  • bVectorsDiffusion gradient vectors, if requested. Will be NA if the information could not be found in the files.

References

Please cite the following reference when using TractoR in your work:

J.D. Clayden, S. Muñoz Maniega, A.J. Storkey, M.D. King, M.E. Bastin & C.A. Clark (2011). TractoR: Magnetic resonance imaging and tractography with R. Journal of Statistical Software 44(8):1-18. http://www.jstatsoft.org/v44/i08/.

See Also

DicomMetadata, MriImage, MriImageMetadata, sortDicomDirectory.