AFNIFileDescriptor-class
                        This class supports the AFNI file format
AFNIMetaInfo            AFNIMetaInfo
AxisSet-class           Virtual base class representing an ordered set
                        of named axes.
AxisSet1D-class         A one-dimensional axis set
AxisSet2D-class         A two-dimensional axis set
AxisSet3D-class         A three-dimensional axis set
AxisSet4D-class         A four-dimensional axis set
AxisSet5D-class         A five-dimensional axis set
BaseMetaInfo-class      This is a base class to represent meta
                        information
BaseSource-class        This is a base class to represent a data source
BinaryReader            BinaryReader
BinaryReader-class      BinaryReader
BinaryWriter-class      BinaryWriter
BrainBucket-class       BrainBucket
BrainBucketSource-class
                        BrainBucketSource
BrainData-class         BrainData
BrainFileDescriptor-class
                        This class represents a neuroimaging file
                        format
BrainFileSource-class   Base class for representing a data source for
                        images. The purpose of this class is to provide
                        a layer in between low level IO and image
                        loading functionality.
BrainMetaInfo-class     This class contains meta information from an
                        image
BrainSlice              BrainSlice constructor
BrainSlice-class        BrainSlice
BrainSource-class       Base class for representing a data source for
                        images. The purpose of this class is to provide
                        a layer in between low level IO and image
                        loading functionality.
BrainSpace              Constructor function for 'BrainSpace' class
BrainSpace-class        BrainSpace
BrainVector-class       Four-dimensional brain image
BrainVectorSource-class
                        BrainVectorSource
BrainVolume-class       Three-dimensional brain image
BrainVolumeSource-class
                        A class is used to produce a 'BrainVolume'
                        instance
ClusteredBrainVolume-class
                        ClusteredBrainVolume
DenseBrainVector-class
                        DenseBrainVector
DenseBrainVolume-class
                        DenseBrainVolume
FileMetaInfo-class      This class contains meta information from an
                        image data file
IndexLookupVolume-class
                        IndexLookupVolume
Kernel                  Create a Kernel object
Kernel-class            Kernel
Layer                   create a Layer object
Layer-class             Layer
LogicalBrainVolume-class
                        LogicalBrainVolume
NIfTIFileDescriptor-class
                        This class supports the NIfTI file format
NIfTIMetaInfo           Constructor for 'NIfTIMetaInfo' class
NamedAxis-class         This class represents an axis with a name
                        attribute
NullMetaInfo-class      This is class is used to denote the absense of
                        meta information
ROIVolume               Create an instance of class ROIVolume
ROIVolume-class         ROIVolume
RandomSearchlight       Create an Random Searchlight iterator
RegionCube              Create A Cuboid Region of Interest
RegionSphere            Create A Spherical Region of Interest
Searchlight             Create an exhaustive searchlight iterator
SparseBrainVector-class
                        SparseBrainVector
SparseBrainVectorSource-class
                        SparseBrainVectorSource
SparseBrainVolume-class
                        SparseBrainVolume
[,ROIVolume,numeric,missing,ANY-method
                        extract data from 'ROIVolume'
[,SparseBrainVector,missing,missing,ANY-method
                        extract data from SparseBrainVector
[,SparseBrainVector,missing,numeric,ANY-method
                        extract data from SparseBrainVector
[,SparseBrainVector,numeric,missing,ANY-method
                        extract data from SparseBrainVector
[,SparseBrainVector,numeric,numeric,ANY-method
                        extract data from SparseBrainVector
[[,BrainBucket,character,missing-method
                        extract labeled volume from 'BrainBucket'
[[,BrainBucket,numeric,missing-method
                        extract indexed volume from 'BrainBucket'
addDim                  Generic function to add a dimension to an
                        object
as                      conversion from ROIVolume to DenseBrainVolume
as.array,BrainData-method
                        convert 'BrainData' instance to array
as.list,SparseBrainVector-method
                        as.list
as.logical,BrainVolume-method
                        as.logical
as.mask                 Convert to a LogicalBrainVolume
as.matrix,BrainData-method
                        convert 'BrainData' instance to matrix
as.matrix,DenseBrainVector-method
                        convert a DenseBrainVector to a matrix
as.numeric,SparseBrainVolume-method
                        Convert SparseBrainVolume to numeric
as.raster,Layer-method
                        as.raster
as.sparse               Convert to sparse representation
as.vector,BrainData,ANY-method
                        convert 'BrainData' instance to vector
axes                    Generic getter function to extract image axes
axisToIndex             Generic function to convert 1-dimensional real
                        axis coordinates along a single axis dimension
                        to an 1D index along the same axis
bounds                  Generic function to extract the spatial bounds
                        (origin + dim * spacing) of an image param x
                        the object
close,BinaryReader-method
                        close
clusterCenters          clusterCenters
concat                  Concatenate two objects
connComp                Find connected components
connComp3D              Extract connected components from a 3D mask
coordToGrid             Generic function to convert N-dimensional real
                        world coordinates to grid coordinates
coordToIndex            Generic function to convert N-dimensional real
                        world coordinates to 1D indices
coords                  Extract coordinates
dataFile                Generic function to get the name of the data
                        file, given a file name and a
                        'BrainFileDescriptor' instance.
dataFileMatches         Generic function to test whether a file name
                        conforms to the given a 'BrainFileDescriptor'
                        instance. Will test for match to data file only
dataReader              Generic function to create data reader
dim,BrainData-method    dim
dropDim                 Generic function to drop a dimension from an
                        object
eachSeries              Generic functions to apply a function to each
                        series of a 4D image That is, if the 4th
                        dimension is 'time' each series is a 1D time
                        series.
eachSlice               Generic functions to apply a function to each
                        (2D) slice of an image
eachVolume              Generic function to apply a function to each
                        volume of a four-dimensional image
fileMatches             Generic function to test whether a file name
                        conforms to the given 'BrainFileDescriptor'
                        instance. Will test for match to either header
                        file or data file
fill                    Generic function to map values from one set to
                        another using a user-supplied lookup table
gridToIndex             Generic function to convert N-dimensional grid
                        coordinate to 1D indices
headerFile              Generic function to get the name of the header
                        file, given a file name and a
                        'BrainFileDescriptor' instance.
headerFileMatches       Generic function to test whether a file name
                        conforms to the given 'BrainFileDescriptor'
                        instance. Will test for match to header file
                        only
image,BrainVolume-method
                        image
indexToCoord            Generic function to convert 1D indices to
                        N-dimensional real world coordinates
indexToGrid             Generic function to convert 1D indices to
                        N-dimensional grid coordinates
indices                 Extract indices
inverseTrans            Generic getter to extract inverse image
                        coordinate transformation
length,BrainVector-method
                        Get length of 'BrainVector'. This is the numbe
                        rof volumes in the volume vector (e.g. the 4th
                        image dimension)
length,ROIVolume-method
                        length
loadBucket              loadBucket
loadData                Generic function to load data from a data
                        source
loadVector              loadVector
loadVolume              load an image volume from a file
loadVolumeList          loadVolList
lookup                  Index Lookup operation
makeVector              makeVector
makeVolume              makeVolume
map                     Generic function to apply a function to an
                        object
matchAnatomy2D          given two named axes return AxisSet2D singleton
matchAnatomy3D          given three named axes return AxisSet3D
                        singleton
mergePartitions         mergePartitions
names,BrainBucketSource-method
                        extract names of 'BrainBucketSource' instance
ndim                    Generic function to extract the number of
                        dimensions of an object
numClusters             numClusters
origin                  Generic getter to extract image origin
overlay                 overlay two objects
partition               partition
permMat                 extract permutation matrix
pick                    pick
print,NamedAxis-method
                        print a 'NamedAxis' instance
readElements            Generic function to read a sequence of elements
                        from an input source
readHeader              read header information of an image file
readMetaInfo            Generic function to read image meta info given
                        a file and a 'BrainFileDescriptor' instance.
series                  Extract vector series from object
seriesIter              Construct a series iterator
show,BrainVolume-method
                        show
slice                   extract a 2D slice from an image volume
space                   Generic function to extract the 'space' member
                        variable
spacing                 Generic function to extract the voxel
                        dimensions of an image
splitFill               Generic function to fill disjoint sets of
                        values with the output of a function
splitReduce             Generic function to summarize subsets of an
                        object
splitScale              Generic function to center/scale subsets of an
                        object
stripExtension          Generic function to strip extension from file
                        name, given a 'BrainFileDescriptor' instance.
takeSeries              Generic function to extract a set of series
                        from a 4D image
takeVolume              Generic function to extract a volume from a
                        four-dimensional image
tesselate               tesselate
trans                   Generic getter to extract image coordinate
                        transformation
voxels                  extract voxel coordinates
writeElements           Generic function to write a sequence of
                        elements from an input source
writeVector             Generic function to write an image vector to
                        disk
writeVolume             Generic function to write an image volume to
                        disk
