# Read, Manipulate and Visualise Magnetic Resonance Images

## Documentation for package ‘tractor.base’ version 3.5.0

- DESCRIPTION file.

## Help Pages

%||% | Resolve a variable to a default when NULL
allEqual | Test whether all elements of a vector are equal
angleBetweenVectors | Miscellaneous vector functions
asDiffusionScheme | Create a DiffusionScheme object from data
asDiffusionScheme.DiffusionScheme | Create a DiffusionScheme object from data
asDiffusionScheme.matrix | Create a DiffusionScheme object from data
asDiffusionScheme.MriImage | Create a DiffusionScheme object from data
asMriImage | Creating MriImage objects from data
augmentedInfoPanel | A simple interactive viewer for MriImage objects
copyImageFiles | Image file sets
createContactSheetGraphic | Visualise MriImage objects
createNeighbourhoodInfo | Image neighbourhoods
createProjectionGraphic | Visualise MriImage objects
createSliceGraphic | Visualise MriImage objects
deduplicate | Concatenate and deduplicate vectors
deserialiseReferenceObject | Reference object serialisation and deserialisation
DicomMetadata | The DicomMetadata class
DicomMetadata-class | The DicomMetadata class
DiffusionScheme | The DiffusionScheme class
DiffusionScheme-class | The DiffusionScheme class
embrace | Combine similar strings into one
emptyMatrix | The empty matrix
ensureFileSuffix | Functions for file name and path manipulation
equivalent | Test two numeric vectors for equivalence
execute | Find or run an external executable file
expandFileName | Functions for file name and path manipulation
extractMriImage | Creating MriImage objects from data
fi | Shorthand anonymous functions
FileMap | The FileMap class
FileMap-class | The FileMap class
FileSet | The FileSet class
FileSet-class | The FileSet class
fillShells | Assign image volumes to shells
fx | Shorthand anonymous functions
fxy | Shorthand anonymous functions
fxyz | Shorthand anonymous functions
getColourScale | Obtaining colour scales
identifyImageFileNames | Resolve image paths
imageFileExists | Image file sets
imageFiles | Image file sets
ImageFileSet | The ImageFileSet class
ImageFileSet-class | The ImageFileSet class
implode | Create a character string by concatenating the elements of a vector
indexList | Extract one or more elements from a list
infix | Resolve a variable to a default when NULL
is.emptyMatrix | The empty matrix
is.nilObject | The nil object
isDeserialisable | Reference object serialisation and deserialisation
locateExecutable | Find or run an external executable file
loso | Lists of serialisable objects
matchPaths | Functions for file name and path manipulation
mergeMriImages | Merging MriImage objects
MriImage | The MriImage class
MriImage-class | The MriImage class
neighbourhoodInfo | Image neighbourhoods
newSparseArrayWithData | Create a SparseArray object
nilObject | The nil object
Optional | Optional types
paths | Functions for file name and path manipulation
pluralise | Number agreement with a vector
polarPlotPanel | A simple interactive viewer for MriImage objects
printLabelledValues | Pretty print labelled information
promote | Promote a vector to a single-column or single-row matrix
readDicomDirectory | Read a directory of DICOM files
readDicomFile | Read a DICOM file into a DicomMetadata object
readDiffusionScheme | Read and write diffusion schemes
readImageFile | Reading and writing image files
registerDeserialiser | Reference object serialisation and deserialisation
registerPathHandler | Functions for file name and path manipulation
relativePath | Functions for file name and path manipulation
removeImageFiles | Image file sets
reorderMriImage | Creating MriImage objects from data
resolvePath | Functions for file name and path manipulation
resolveVector | Miscellaneous vector functions
SerialisableObject | The SerialisableObject class
SerialisableObject-class | The SerialisableObject class
serialisation | Reference object serialisation and deserialisation
serialiseReferenceObject | Reference object serialisation and deserialisation
sortDicomDirectories | Sort a directory of DICOM files into series
SparseArray | The SparseArray class
SparseArray-class | The SparseArray class
symlinkImageFiles | Image file sets
threadSafeTempFile | Obtain thread-safe temporary file names
TractorObject | The TractorObject class
TractorObject-class | The TractorObject class
trimMriImage | Creating MriImage objects from data
vectorCrossProduct | Miscellaneous vector functions
vectorLength | Miscellaneous vector functions
viewImages | A simple interactive viewer for MriImage objects
visualisation | Visualise MriImage objects
where | Compact conditional values
writeDiffusionScheme | Read and write diffusion schemes
writeImageFile | Reading and writing image files
[-method | Indexing methods
[<--method | Indexing methods