# Read, Manipulate and Visualise Magnetic Resonance Images

## Documentation for package ‘tractor.base’ version 3.3.3.1

- 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
asMriImage | Creating MriImage objects from data
copyImageFiles | Working with MRI images stored in NIfTI, Analyze and MGH formats
createContactSheetGraphic | Visualise MriImage objects
createNeighbourhoodInfo | Image neighbourhoods
createProjectionGraphic | Visualise MriImage objects
createSliceGraphic | Visualise MriImage objects
deduplicate | Concatenate and deduplicate vectors
defaultInfoPanel | A simple interactive viewer for MriImage objects
deserialiseReferenceObject | Reference object serialisation and deserialisation
DicomMetadata | The DicomMetadata class
DicomMetadata-class | The DicomMetadata 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
extractDataFromMriImage | Deprecated functions
extractMriImage | Creating MriImage objects from data
fi | Shorthand anonymous functions
fx | Shorthand anonymous functions
fxy | Shorthand anonymous functions
fxyz | Shorthand anonymous functions
getColourScale | Obtaining colour scales
identifyImageFileNames | Working with MRI images stored in NIfTI, Analyze and MGH formats
imageFileExists | Working with MRI images stored in NIfTI, Analyze and MGH formats
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
matchPaths | Functions for file name and path manipulation
mergeMriImages | Merging MriImage objects
MriImage | The MriImage class
MriImage-class | The MriImage class
neighbourhoodInfo | Image neighbourhoods
newDicomMetadataFromFile | Deprecated functions
newMriImageByExtraction | Deprecated functions
newMriImageByMasking | Deprecated functions
newMriImageByReordering | Deprecated functions
newMriImageByThresholding | Deprecated functions
newMriImageByTrimming | Deprecated functions
newMriImageFromDicomDirectory | Deprecated functions
newMriImageFromFile | Deprecated functions
newMriImageWithBinaryFunction | Deprecated functions
newMriImageWithData | Deprecated functions
newMriImageWithSimpleFunction | Deprecated functions
newSparseArrayWithData | Create a SparseArray object
nilObject | The nil object
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
readImageFile | Working with MRI images stored in NIfTI, Analyze and MGH formats
registerDeserialiser | Reference object serialisation and deserialisation
registerPathHandler | Functions for file name and path manipulation
relativePath | Functions for file name and path manipulation
removeImageFiles | Working with MRI images stored in NIfTI, Analyze and MGH formats
removeImageFilesWithName | Deprecated functions
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 | Working with MRI images stored in NIfTI, Analyze and MGH formats
threadSafeTempFile | Obtain thread-safe temporary file names
timeSeriesPanel | A simple interactive viewer for MriImage objects
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
writeImageFile | Working with MRI images stored in NIfTI, Analyze and MGH formats
writeMriImageToFile | Deprecated functions
[-method | Indexing methods
[<--method | Indexing methods