tractor.base-deprecated: Deprecated functions
In tractor.base: Read, Manipulate and Visualise Magnetic Resonance Images

newMriImageFromDicomDirectory

R Documentation

Deprecated functions

Description

These functions are deprecated, generally in favour of more succint alternatives.

Usage

newMriImageFromDicomDirectory(dicomDir, readDiffusionParams = FALSE,
  untileMosaics = TRUE)

newMriImageFromFile(fileName, fileType = NULL, metadataOnly = FALSE,
  volumes = NULL, sparse = FALSE, mask = NULL, reorder = TRUE)

writeMriImageToFile(image, fileName = NULL, fileType = NA, overwrite = TRUE)

newMriImageByExtraction(image, dim, loc)

extractDataFromMriImage(image, dim, loc)

newMriImageByReordering(image)

newMriImageByTrimming(image, clearance = 4)

newMriImageWithData(data, templateImage = nilObject(), imageDims = NA,
  voxelDims = NA, voxelDimUnits = NA, origin = NA, tags = NA)

newMriImageWithSimpleFunction(image, fun, ...)

newMriImageWithBinaryFunction(image1, image2, fun, ...)

newMriImageByMasking(image, mask)

newMriImageByThresholding(image, level, defaultValue = 0)

newDicomMetadataFromFile(fileName, checkFormat = TRUE, dictionary = NULL,
  stopTag = NULL, ignoreTransferSyntax = FALSE)

removeImageFilesWithName(fileName)

Arguments

`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?
`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`.
`fileName`	File names, with or without appropriate extension.
`fileType`	A character vector of length one, giving the file type required or expected. If this option is missing, the file type used for writing images will be taken from the `tractorFileType` option. See Details.
`metadataOnly`	Logical value: if `TRUE`, only metadata are read into the object.
`volumes`	An optional integer vector specifying a subset of volumes to read (generally to save memory). If given, only the requested volumes in the 4D file will be read.
`sparse`	Logical value: should the image data be stored in a `SparseArray` object?
`mask`	An array whose nonzero voxel locations will be masked in.
`reorder`	Logical value: should the image data be reordered to LAS? This is recommended in most circumstances.
`image, image1, image2`	`MriImage` objects.
`overwrite`	Logical value: overwrite an existing image file? For `writeImageFile`, an error will be raised if there is an existing file and this is set to FALSE.
`dim`	The dimension and location along that dimension for which data should be extracted.
`loc`	The dimension and location along that dimension for which data should be extracted.
`clearance`	The number of voxels' clearance left around a trimmed image.
`data`	An array of pixel/voxel data.
`templateImage`	An optional `MriImage` object, to be used as a metadata template.
`imageDims`	Metadata for the new image object. These values override any from the metadata object or data array. See `MriImage` class documentation for details.
`voxelDims`	Metadata for the new image object. These values override any from the metadata object or data array. See `MriImage` class documentation for details.
`voxelDimUnits`	Metadata for the new image object. These values override any from the metadata object or data array. See `MriImage` class documentation for details.
`origin`	Metadata for the new image object. These values override any from the metadata object or data array. See `MriImage` class documentation for details.
`tags`	Metadata for the new image object. These values override any from the metadata object or data array. See `MriImage` class documentation for details.
`fun`	A function, of the appropriate arity.
`...`	Additional argument to `fun`.
`level`	The threshold level, below which all voxels will be reset.
`defaultValue`	The value to reset to.
`checkFormat`	If `TRUE`, the function will check for the magic string `"DICM"` at byte offset 128. This string should be present, but in reality not all files contain it.
`dictionary`	Ignored.
`stopTag`	An integer vector giving the group and element numbers (in that order) of a DICOM tag, or `NULL`. If not `NULL`, the function will stop parsing the DICOM file if the specified tag is encountered. This can be used to speed up the process if a specific tag is required.
`ignoreTransferSyntax`	If `TRUE`, any transfer syntax stored in the file will be ignored, and the code will try to deduce the transfer syntax using heuristics. This may occasionally be necessary for awkward DICOM files, but is not generally recommended.