The DicomMetadata class

Description

This class represents DICOM metadata, which typically contains detailed information about the scan parameters and subject.

Fields

source

String naming the source file

tags

Data frame of tag information

tagOffset

Starting offset for tags in the file

dataOffset

Starting offset for pixel data in the file

dataLength

Pixel data length

explicitTypes

Logical value indicating whether explicit types are used in the file

endian

String naming the endianness of the file

asciiFields

Character vector containing the contents of the ASCII header, if requested and present in the file.

transferSyntax

Transfer syntax string, if specified in the file; otherwise the empty string.

Methods

getAsciiFields(regex = NULL)

Retrieve the value of one or more fields in the ASCII header. Returns NA if no fields match

getTagValue(group, element)

Retrieve the value of a given tag, using an appropriate R type. Returns NA if the tag is missing

The MriImage class

Description

This class represents an MRI image. An object of this class is made up of some voxel data, stored as a sparse or dense numeric array, and some metadata, such as the file it was read from, the voxel dimensions, and so on. The group generic functions Math, Ops and Summary are defined for this class, as are methods for coercing to and from a standard array.

Fields

imageDims

Integer vector of dimensions

voxelDims

Numeric vector of pixel/voxel spacings

voxelDimUnits

Character vector of spatial and/or temporal spacing units. Millimetres and seconds (i.e., c("mm","s")) are typical

source

String naming the file(s) that the image was read from. This is reset to the empty string if the image is modified

origin

Numeric vector giving the spatial coordinate origin

xform

Numeric matrix giving the NIfTI-style xform matrix associated with the image, which indicates its orientation

reordered

Logical value indicating whether the image has been reordered. See reorderMriImage

tags

Named list of arbitrary DICOM-style tags

data

Sparse or dense array of data, or NULL

Methods

apply(...)

Apply a function to the margins of the image

binarise()

Binarise the image by setting nonzero values to one

fill(value)

Fill the image with a particular value

find(fun = NULL, ..., array = TRUE)

Find voxels whose values are not zero, or satisfy a function

getDataAtPoint(...)

Obtain the value of the image at a particular point

getMetadata()

Obtain a version of the image with any data removed

getNonzeroIndices(array = TRUE, positiveOnly = FALSE)

Find voxels whose values are not zero

getSlice(dim, loc)

Extract data from a slice of the image along one dimension

getSparseness()

Obtain the proportion of zeroes in the image

getTags(keys = NULL)

Retrieve some or all of the tags stored with the image

getXform(implicit = TRUE)

Retrieve the stored or implicit xform matrix

map(fun, ..., sparse = NULL)

Replace the current data with the result of a function

mask(maskImage)

Mask the image, setting zero voxels in the mask to zero

setData(newData)

Replace the data in the image

setOrigin(newOrigin)

Update the origin of the image

setSource(newSource)

Update the source of the image

setTags(..., merge = FALSE)

Add, replace or merge metadata tags

setXform(newXform)

Update the xform matrix associated with the image

summarise()

Summarise key aspects of the object

threshold(level, defaultValue = 0)

Threshold the image by setting values below the threshold level to zero

The SerialisableObject class

Description

This reference class extends TractorObject by adding a function for simple serialisation of the data fields of an object, either to a list or a file. This is intended to be used for classes whose state can meaningfully be restored from a list of standard R objects (not including transient C/C++ pointers, for example). A serialised object may be deserialised using the deserialiseReferenceObject function.

Methods

serialise(file = NULL)

Serialise the object to a list or file

See Also

save

The SparseArray class

Description

This class represents an array with any number of dimensions, in which a significant proportion of entries are zero. The coordinates of nonzero entries are stored along with their values, with all remaining entries assumed to be zero. Methods are provided to index into the array in the standard way, using matrix or vector indices; and for coercing between SparseArray objects and standard (dense) arrays.

Fields

data

Vector of nonzero data values

coords

Integer matrix of nonzero data locations, one per row

dims

Integer vector of dimensions

Methods

aperm(perm)

Permute the dimensions of the array

apply(margin, fun, ...)

Apply a function to margins of the array

flip(dimsToFlip)

Flip the array along one or more directions

setCoordinatesAndData(newCoords, newData)

Update the nonzero locations and data values in the array

setDimensions(newDims)

Change the dimensions of the image

summarise()

Summarise key aspects of the object

The TractorObject class

Description

This reference class extends the standard envRefClass class, adding methods for finding all of the field or methods available for an object. There is also a method for summarising key elements of the object as a named character vector, which can be suitable overridden by inheriting classes. The show method prints this summary as a labelled list.

Methods

fields()

Retrieve a list of all field names

methods()

Retrieve a list of all method names

summarise()

Summarise key aspects of the object

Indexing methods

Description

Indexing methods for SparseArray and MriImage objects. For the latter class, arguments are passed to the equivalents for array or SparseArray, except where i is another MriImage object, where its nonzero region will be used to provide the indices. For SparseArray, indexing may be blank, or by numeric vector or matrix.

Usage

## S4 method for signature 'SparseArray,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 replacement method for signature 'SparseArray,ANY,ANY'
x[i, j, ...] <- value

## S4 method for signature 'MriImage,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MriImage,ANY,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MriImage,missing,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MriImage,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MriImage,MriImage,missing'
x[i, j, ..., drop = TRUE]

## S4 replacement method for signature 'MriImage,missing,missing'
x[i, j, ...] <- value

## S4 replacement method for signature 'MriImage,ANY,missing'
x[i, j, ...] <- value

## S4 replacement method for signature 'MriImage,missing,ANY'
x[i, j, ...] <- value

## S4 replacement method for signature 'MriImage,ANY,ANY'
x[i, j, ...] <- value

## S4 replacement method for signature 'MriImage,MriImage,missing'
x[i, j, ...] <- value

Arguments

Value

A vector, array or SparseArray.

Author(s)

Jon Clayden

Test whether all elements of a vector are equal

Description

This function tests whether all elements of the specified vector are equal to each other, i.e., whether the vector contains only a single unique value. For lists, equality is determined using equivalent.

Usage

allEqual(x, ignoreMissing = FALSE, ...)

Arguments

Value

TRUE if all elements test equivalent; FALSE otherwise.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

equivalent for elementwise equivalence of two vectors.

Examples

allEqual(c(1,1,1))  # TRUE
allEqual(c(1,1,NA))  # FALSE
allEqual(c(1,1,NA), ignoreMissing=TRUE)  # TRUE

Creating MriImage objects from data

Description

Functions for creating MriImage objects from data, including other images. All of these functions use data from arrays or MriImage objects to create a new MriImage object. asMriImage is the basic fucntion for creating an object from its constituents: an array of voxel values and some metadata (and/or a template image).

Usage

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

extractMriImage(image, dim, loc)

trimMriImage(image, clearance = 4, indices = NULL)

reorderMriImage(image)

Arguments

Details

extractMriImage reduces the dimensionality of the source image by one, by extracting a single “slice” of data along one dimension. trimMriImage trims empty space from the edges of an image, reducing the dimensions of the image and thus avoiding the storage of lots of zeroes. reorderMriImage reorders the image data (and corresponding metadata) to the LAS convention, an operation which is usually performed when an image is read from file.

Value

An MriImage object.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

MriImage

A simple interactive viewer for MriImage objects

Description

The viewImages function provides a simple interactive viewer for MriImage objects. 3D and 4D images may be used.

Usage

augmentedInfoPanel(indexNames = NULL)

polarPlotPanel(directions, bValues = NULL)

viewImages(images, colourScales = NULL, point = NULL, interactive = TRUE,
  crosshairs = TRUE, orientationLabels = TRUE,
  infoPanel = RNifti::defaultInfoPanel, ...)

Arguments

Value

These functions are called for their side effects.

Note

The defaultInfoPanel and timeSeriesPanel functions are not intended to be called directly. They are simple examples of valid values for the infoPanel argument to viewImages.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

getColourScale

Image neighbourhoods

Description

This function calculates information about a cuboidal region of an image, with a centre and a fixed voxel width.

Usage

createNeighbourhoodInfo(width, dim = 3, centre = rep(0, dim))

Arguments

Value

createNeighbourhoodInfo returns a list with class "neighbourhoodInfo" and elements

width

Copied from the width argument.

dim

Copied from the dim argument.

centre

Copied from the centre argument.

vectors

dim x width^dim matrix whose columns give the locations of each point in the neighbourhood.

innerProducts

A square, symmetric matrix of inner products between every location in the neighbourhood and every other.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

Visualise MriImage objects

Description

Visualise MriImage objects noninteractively using an R graphics device. See viewImages for an interactive alternative. These functions create 2D visualisations of 3D images by slicing or maximum intensity projection.

Usage

createSliceGraphic(image, x = NA, y = NA, z = NA,
  device = c("internal", "png"), colourScale = 1, add = FALSE,
  file = NULL, zoomFactor = 1, windowLimits = NULL)

createProjectionGraphic(image, axis, device = c("internal", "png"),
  colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1,
  windowLimits = NULL)

createContactSheetGraphic(image, axis, device = c("internal", "png"),
  colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1,
  windowLimits = NULL, clearance = NULL, nColumns = NULL)

Arguments

Value

These functions are called for their side effects.

Note

When the device option is set to "png", the "png" and "mmand" packages are required by these functions.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

See viewImages for an interactive alternative, and getColourScale for details of how colour scales are specified. Also image, which is used as the underlying plot function.

Concatenate and deduplicate vectors

Description

This function returns its arguments, after concatenating them using c and then removing elements with duplicate names. The first element with each name will remain, possibly with subsequent elements' content appended to it. Unnamed elements are retained.

Usage

deduplicate(..., merge = FALSE)

Arguments

Value

The concatenated and deduplicated vector.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

Combine similar strings into one

Description

Merge a vector of strings with a common prefix and/or suffix into one string with the unique parts in braces, comma-separated.

Usage

embrace(strings)

Arguments

Value

A single merged string, with the common prefix and suffix as attributes.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

Examples

embrace(c("image.hdr", "image.img"))

The empty matrix

Description

The empty matrix is a standard matrix of dimensions 0 x 0. It is intended to be used as a placeholder where a matrix is required but no information is stored.

Usage

emptyMatrix()

is.emptyMatrix(object)

Arguments

Value

emptyMatrix returns the empty matrix, equivalent to matrix(NA,0,0). is.emptyMatrix returns TRUE if its argument is identical to the empty matrix.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

Test two numeric vectors for equivalence

Description

This function is a wrapper for isTRUE(all.equal(x,y,...{})), but with the additional capability of doing sign-insensitive comparison.

Usage

equivalent(x, y, signMatters = TRUE, ...)

Arguments

Value

TRUE if all elements of x match all elements of y to within tolerance, ignoring signs if required. FALSE otherwise.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

all.equal

Examples

equivalent(c(-1,1), c(1,1))  # FALSE
equivalent(c(-1,1), c(1,1), signMatters=FALSE)  # TRUE
equivalent(1:2, 2:3, tolerance=2)  # TRUE

Shorthand anonymous functions

Description

These functions provide a shorthand route to simple anonymous functions.

Usage

fx(expr)

fxy(expr)

fxyz(expr)

fi(expr)

Arguments

Value

The function constructed.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

Obtaining colour scales

Description

The getColourScale function can be used to obtain a standard or customised colour scale for use in the package's image visualisation functions.

Usage

getColourScale(n)

Arguments

Details

Colour scales can be specified in any of three ways. Firstly, by a single number, representing a predefined colour scale. Currently valid values are 1 (greyscale, black background), 2 (red to yellow heat scale, red background), 3 (blue to red rainbow scale, blue background), 4 (blue to white to red diverging scale, white background), 5 (white to red, white background), 6 (white to blue, white background), 7 (yellow to orange to red) and 8 (purple to green to yellow, perceptually uniform). Secondly, a single colour name can be given (see colours); in this case the background will be black. This is useful for binary images. Thirdly, and most flexibly, a list with two named elements can be given: colours, a vector of colours representing the colour scale, perhaps created using using the shades package; and background, a single colour representing the background.

Value

A list with elements

colours

A character-mode vector representing the colours in the scale, usually of length 100. This can be passed as a colour scale to R's plotting functions.

background

A single character string representing the background colour.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

colours, rgb, colorRamp, and the shades package for colour manipulation.

Examples

getColourScale(1)

Working with MRI images stored in various formats

Description

Functions for reading, writing, locating, copying and removing MRI images stored in NIfTI, Analyze, MGH and MRtrix formats.

Usage

identifyImageFileNames(fileName, fileType = NULL, errorIfMissing = TRUE,
  auxiliaries = c("dirs", "lut", "tags"), ...)

imageFileExists(fileName, fileType = NULL)

removeImageFiles(fileName, ...)

symlinkImageFiles(from, to, overwrite = FALSE, relative = TRUE, ...)

copyImageFiles(from, to, overwrite = FALSE, deleteOriginals = FALSE, ...)

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

writeImageFile(image, fileName = NULL, fileType = NA, overwrite = TRUE,
  datatype = "fit", writeTags = FALSE)

Arguments

Details

NIfTI and Analyze are related formats for storing magnetic resonance images. NIfTI is a more recent extension of Analyze, and contains more specific information about, for example, the orientation of the image. Its use is therefore recommended where possible. MGH format is used by the popular image processing package FreeSurfer, and MRtrix format by the software of the same name. These formats use a number of different file extensions, but the details are abstracted away from the user by these functions.

TractoR does not allow for files with the same basic name using multiple Analyze/NIfTI/MGH/MRtrix formats in a single directory (e.g. "foo.nii" AND "foo.img"), and these functions will produce an error if multiple compatible files exist.

Suitable values for fileType (and the tractorFileType option, which is used as a default for writing) are "NIFTI", "NIFTI_PAIR" (the two-file NIfTI format), "MGH", and corresponding gzipped versions of these with "_GZ" appended. File types "ANALYZE" and "MRTRIX", and "_GZ" variants, are additionally available for reading only. "NIFTI_GZ" is the default value for the tractorFileType option, but that can be changed using a call to options, or by setting the TRACTOR_FILETYPE environment variable before loading the tractor.base package.

Since multiple files may be involved, copying, moving or symlinking images is not trivial. copyImageFiles and symlinkImageFiles are wrappers around the standard functions file.copy and file.symlink which handle this complexity.

Value

readImageFile returns an MriImage object. imageFileExists returns TRUE if an existing file with the specified name exists (all file extensions are checked), and FALSE otherwise. removeImageFiles returns the result of unlink applied to all relevant files. writeImageFile and identifyImageFileNames return a list with the following elements, describing the identified or written files:

fileStem

The file name without extension.

headerFile

The full header file name.

imageFile

The full image file name.

format

The format of the files ("Nifti", "Analyze" or "Mgh"). Not returned by writeImageFile.

copyImageFiles and symlinkImageFiles are called for their side effects.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

The NIfTI-1 standard (http://nifti.nimh.nih.gov/nifti-1) and MriImage.

Create a character string by concatenating the elements of a vector

Description

Create a character string by concatenating the elements of a vector, using a separator and optional final separator.

Usage

implode(strings, sep = "", finalSep = NULL, ranges = FALSE)

Arguments

Value

A character vector of length one.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

paste

Examples

implode(1:3, ", ")  # "1, 2, 3"
implode(1:3, ", ", " and ")  # "1, 2 and 3"
implode(1:2, ", ", " and ")  # "1 and 2"
implode(1:3, ", ", ranges=TRUE)  # "1-3"

Extract one or more elements from a list

Description

Given a list-like first argument, this function extracts one or more of its elements. Numeric and character indexing are allowed.

Usage

indexList(list, index = NULL)

Arguments

Value

If index is NULL, the whole list is returned. Otherwise, if index has length one, the corresponding element is extracted and returned. Otherwise a list containing the requested subset is returned.

Note

This function is not type-safe, in the sense that its return type depends on its arguments. It should therefore be used with care.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

Resolve a variable to a default when NULL

Description

This is a very simple infix function for the common TractoR idiom whereby NULL is used as a default argument value, but later needs to be resolved to a meaningful value if not overridden in the call. It returns its first argument unless it is NULL, in which case it falls back on the second argument.

Usage

X %||% Y

Arguments

Value

X, if it is not NULL; otherwise Y.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

where, which resolves a value if an expression is TRUE. Several calls to that function can be conveniently chained together with this one.

Reference object serialisation and deserialisation

Description

Rather than using R's save and load functions directly for reference objects, TractoR uses the SerialisableObject class and these functions to save and load objects. The main difference is that this approach stores only the data in the object, and not the functions which operate on them. This helps backward compatibility when new member functions are added.

Usage

isDeserialisable(object, expectedClass = NULL)

serialiseReferenceObject(object, file = NULL)

deserialiseReferenceObject(file = NULL, object = NULL, raw = FALSE)

registerDeserialiser(className, deserialiser)

Arguments

Details

The serialiseReferenceObject function, or the serialise member function of the SerialisableObject class can be used to create and/or save a version of an object which contains a hierarchical representation of the data embedded in it. These serialised objects are standard R lists, with an "originalClass" attribute describing the class of the original object. The deserialiseReferenceObject function can be used to deserialise them. Custom deserialisers can be specified using registerDeserialiser, typically for legacy classes.

Note that this should generally NOT be used as the primary mechanism for saving and loading MriImage objects. Saving to standard NIfTI/Analyze format is usually preferable, and can be done using writeImageFile.

Value

isDeserialisable returns TRUE if the object is deserialisable and inherits from the specified class. deserialiseReferenceObject returns a raw or reconstituted object after deserialisation.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

SerialisableObject, save, load, writeImageFile.

Find or run an external executable file

Description

The execute function is a wrapper around the system2 function in base, which additionally echoes the command being run (including the full path to the executable) if the reportr output level is Debug. locateExecutable simply returns the path to an executable file on the system PATH.

Usage

locateExecutable(fileName, errorIfMissing = TRUE)

execute(executable, params = NULL, errorOnFail = TRUE, silent = FALSE,
  ...)

Arguments

Value

For execute, the return value of the underlying call to system2. For locateExecutable, the location of the requested executable, or NULL if it could not be found.

Note

These functions are designed for Unix systems and may not work on Windows.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

system2

Merging MriImage objects

Description

This function concatenates the data from a series of MriImage objects, and then attempts to work out the final dimensions of the merged image and returns it.

Usage

mergeMriImages(..., bindDim = NULL, padTags = FALSE)

Arguments

Value

A merged image.

Note

Tags are retained as-is if they are identical in each image. Otherwise they are concatenated if their lengths match the number of blocks in each image, or concatenated with NAs for missing values if padTags is TRUE.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

MriImage

Create a SparseArray object

Description

This function creates a SparseArray object from its constituent parts.

Usage

newSparseArrayWithData(data, coordinates, dims)

Arguments

Value

A SparseArray object.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

The nil object

Description

The nil object is an empty object of class SerialisableObject. It can be used as a placeholder where such an object of this class, or one of its subclasses, is required. It serialises to the empty list.

Usage

nilObject()

is.nilObject(object)

Arguments

Value

nilObject returns the nil object. is.nilObject returns TRUE if its argument is identical to the nil object, or if it is equivalent in the sense of serialising to an identical result.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

SerialisableObject

Number agreement with a vector

Description

This function chooses the singular or plural form of a word based on the length of an associated vector, or an integer.

Usage

pluralise(singular, x = NULL, n = NULL, plural = NULL)

Arguments

Value

Either singular or plural, as appropriate.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

Pretty print labelled information

Description

This is a simple function to print a series of labels and associated data values, or key-value pairs.

Usage

printLabelledValues(labels, values, outputLevel = OL$Info,
  leftJustify = FALSE)

Arguments

Value

This function is called for its side effect.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

setOutputLevel for the reportr output level system.

Promote a vector to a single-column or single-row matrix

Description

The promote function promotes a vector argument to a single-column or single-row matrix. Matrix arguments are returned unmodified.

Usage

promote(x, byrow = FALSE)

Arguments

Value

A matrix version of the x argument.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

matrix

Read a directory of DICOM files

Description

This function scans a directory for files in DICOM format, and converts them to a single Analyze/NIfTI-format image of the appropriate dimensionality.

Usage

readDicomDirectory(dicomDir, method = c("internal", "divest"),
  readDiffusionParams = FALSE, untileMosaics = TRUE, ...)

Arguments

Value

A list containing elements

image

An MriImage object.

bValues

Diffusion b-values, if requested. Will be NA if the information could not be found in files.

bVectors

Diffusion gradient vectors, if requested. Will be NA if the information could not be found in the files.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

DicomMetadata, MriImage, sortDicomDirectories.

Read a DICOM file into a DicomMetadata object

Description

This function reads a DICOM file into a DicomMetadata object. Only DICOM files from magnetic resonance scanners are supported.

Usage

readDicomFile(fileName, checkFormat = TRUE, stopTag = NULL,
  ignoreTransferSyntax = FALSE, ascii = TRUE)

Arguments

Value

readDicomFile returns a DicomMetadata object, or NULL on failure.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

The DICOM standard, found online at https://www.dicomstandard.org/. (Warning: may produce headaches!) Also readDicomDirectory for information on how to create MriImage objects from DICOM files.

Functions for file name and path manipulation

Description

Functions for expanding file paths, finding relative paths and ensuring that a file name has the required suffix.

Usage

resolvePath(path, ...)

relativePath(path, referencePath)

matchPaths(path, referencePath)

registerPathHandler(regex, handler)

expandFileName(fileName, base = getwd())

ensureFileSuffix(fileName, suffix, strip = NULL)

Arguments

Details

The resolvePath function passes its arguments elementwise through any matching path handler, and returns the resolved paths. Nonmatching elements are returned as-is. registerPathHandler registers a new path handler for special syntaxes, and is for advanced use only. relativePath returns the specified path, expressed relative to referencePath. matchPaths resolves a vector of paths against a vector of reference paths. expandFileName returns the full path to the specified file name, collapsing ".." elements if appropriate. ensureFileSuffix returns the specified file names with the requested suffixes appended (if they are not already).

Value

A character vector.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

normalizePath does most of the work for expandFileName.

Miscellaneous vector functions

Description

These functions provide the (Euclidean) length of a vector, the vector cross product or angle between two vectors.

Usage

resolveVector(len, ...)

vectorLength(vector)

vectorCrossProduct(a, b)

angleBetweenVectors(v1, v2)

Arguments

Value

For vectorLength, the Euclidean norm or length of the specified vector, given by sqrt(sum(vector^2)). For vectorCrossProduct, the vector cross product of the two specified vectors; and for angleBetweenVectors, the angle (in radians) between the two specified vectors. The resolveVector function concatenates the values given in ...{}, and if the result is a vector of length len then it is returned. If not, NULL is returned.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

crossprod for the matrix cross product.

Sort a directory of DICOM files into series

Description

This function sorts a directory containing DICOM files into subdirectories by series UID (DICOM tag 0x0020,0x000e), subject name (0x0010,0x0010) and/or scan date (0x0008,0x0020). Each unique identifier, together with its description for series, will be used as the name for a new subdirectory, and all relevant files will be copied into that subdirectory. Duplicate file names are disambiguated if necessary.

Usage

sortDicomDirectories(directories, method = c("internal", "divest"),
  deleteOriginals = FALSE, sortOn = "series", seriesId = c("UID",
  "number", "time"), nested = TRUE, ...)

Arguments

Value

This function is called for its side effect.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

readDicomDirectory for reading DICOM files into an MriImage object.

Obtain thread-safe temporary file names

Description

This function is a wrapper around tempfile, which creates temporary file names whose path contains the process ID of the calling process. This avoids clashes between threads created by functions such as mclapply (in the “parallel” package), which can easily occur with the standard tempfile function.

Usage

threadSafeTempFile(pattern = "file")

Arguments

Value

A character vector of temporary file names. No files are actually created.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

tempfile

Compact conditional values

Description

This simple function checks whether its first argument is a logical value that evaluates to TRUE. If so, it returns its second argument. If not, it returns its third argument.

Usage

where(condition, value, fallback = NULL)

Arguments

Details

This function differs from the standard ifelse function in that it does not act elementwise, and that the third argument is optional, defaulting to NULL.

Value

value, if condition evaluates to TRUE; otherwise fallback.

Author(s)

Jon Clayden

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. doi:10.18637/jss.v044.i08.

See Also

ifelse