AFNIFileDescriptor-class
                        AFNIFileDescriptor
AFNIMetaInfo            AFNIMetaInfo
AxisSet-class           Base
AxisSet1D-class         AxisSet1D
AxisSet2D-class         AxisSet2D
AxisSet3D-class         AxisSet3D
AxisSet4D-class         AxisSet4D
AxisSet5D-class         AxisSet5D
Base-class              Base
BaseMetaInfo-class      BaseMetaInfo
BaseSource-class        BaseSource
BinaryReader            BinaryReader
BinaryReader-class      BinaryReader
BinaryWriter-class      BinaryWriter
BootstrapSearchlight    Create a searchlight iterator that samples
                        regions from within a mask. Searchlight centers
                        are sampled *without* replacement, but the same
                        voxel can belong to multiple searchlight
                        samples. It is in the latter sense that this is
                        a bootstrap resampling scheme.
BrainBucket-class       BrainBucket
BrainBucketSource-class
                        BrainBucketSource
BrainData-class         BrainData
BrainFileDescriptor-class
                        BrainFileDescriptor
BrainFileSource-class   BrainFileSource 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     BrainMetaInfo This class contains meta
                        information from an image
BrainSlice              BrainSlice constructor
BrainSlice-class        BrainSlice
BrainSource-class       BrainSource
BrainSpace              Constructor function for 'BrainSpace' class
BrainSpace-class        BrainSpace
BrainSurface-class      BrainSurface
BrainSurfaceSource-class
                        BrainSurfaceSource
BrainSurfaceVector-class
                        BrainSurfaceVector
BrainSurfaceVectorSource-class
                        BrainSurfaceVectorSource
BrainVector-class       BrainVector
BrainVectorSource       BrainVectorSource
BrainVectorSource-class
                        BrainVectorSource
BrainVolume             BrainVolume
BrainVolume-class       Base class for image representing 3D volumetric
                        data.
BrainVolumeSource-class
                        BrainVolume BrainVolumeSource A class is used
                        to produce a 'BrainVolume' instance
ClusteredBrainVolume-class
                        ClusteredBrainVolume
ColumnReader            ColumnReader
ColumnReader-class      ColumnReader
DenseBrainVector-class
                        DenseBrainVector
DenseBrainVolume-class
                        DenseBrainVolume
FileMetaInfo-class      FileMetaInfo
FreesurferAsciiSurfaceFileDescriptor-class
                        FresurferAsciiSurfaceFileDescriptor
FreesurferSurfaceGeometryMetaInfo-class
                        FreeSurferSurfaceGeometryMetaInfo This class
                        contains meta information for brain surface
                        geometry
IndexLookupVolume-class
                        IndexLookupVolume
Kernel                  Create a Kernel object
Kernel-class            Kernel
Layer                   Layer
Layer-class             Layer
LogicalBrainVolume-class
                        LogicalBrainVolume
MNI_SPACE_1MM           MNI SPACE 1MM
NIMLSurfaceDataMetaInfo
                        Constructor for 'NIMLSurfaceDataMetaInfo' class
NIMLSurfaceDataMetaInfo-class
                        NIMLSurfaceDataMetaInfo This class contains
                        meta information for surface-based data for the
                        NIML data format
NIMLSurfaceFileDescriptor-class
                        NIMLSurfaceFileDescriptor
NIfTIFileDescriptor-class
                        NIfTIFileDescriptor
NIfTIMetaInfo           Constructor for 'NIfTIMetaInfo' class
NamedAxis-class         NamedAxis
NullMetaInfo-class      NullMetaInfo
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
RegionSquare            Create a square region of interest where the
                        z-dimension is fixed at one voxel coordinate.
Searchlight             Create an exhaustive searchlight iterator
SparseBrainVector-class
                        SparseBrainVector
SparseBrainVectorSource-class
                        SparseBrainVectorSource
SparseBrainVolume-class
                        SparseBrainVolume
SurfaceDataMetaInfo     Constructor for 'SurfaceDataMetaInfo' class
SurfaceDataMetaInfo-class
                        SurfaceDataMetaInfo This class contains meta
                        information for surface-based data (the values
                        that map to a surface geometry)
SurfaceGeometryMetaInfo
                        Constructor for 'SurfaceGeometryMetaInfo' class
SurfaceGeometryMetaInfo-class
                        SurfaceGeometryMetaInfo This class contains
                        meta information for brain surface geometry
[,BrainBucket,index,missing,ANY-method
                        extract labeled volume from 'BrainBucket'
[,ROIVolume,numeric,missing,ANY-method
                        extract data from 'ROIVolume'
[,SparseBrainVector,missing,missing,ANY-method
                        extractor
[,SparseBrainVector,missing,numeric,ANY-method
                        extractor
[,SparseBrainVector,numeric,missing,ANY-method
                        extractor
[,SparseBrainVector,numeric,numeric,ANY-method
                        extractor
[,SparseBrainVolume,matrix,missing,ANY-method
                        extractor
[,SparseBrainVolume,missing,missing,ANY-method
                        extractor
[,SparseBrainVolume,missing,numeric,ANY-method
                        extractor
[,SparseBrainVolume,numeric,missing,missing-method
                        extractor
[,SparseBrainVolume,numeric,numeric,ANY-method
                        extractor
[[,BrainBucket,index,missing-method
                        extract labeled volume from 'BrainBucket'
addDim                  Generic function to add a dimension to an
                        object
as                      conversion from DenseBrainVolume to array
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,SparseBrainVector-method
                        as.matrix
as.numeric,SparseBrainVolume-method
                        Convert SparseBrainVolume to numeric
as.raster,Layer-method
                        as.raster
as.sparse               Convert to from dense to sparse representation
as.vector,BrainData-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 of 'BrainData' object
dim,BrainSpace-method   dim
dim,FileMetaInfo-method
                        dim of 'FileMetaInfo'
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
gridToCoord             Generic function to convert N-dimensional grid
                        coordinate coordinates to real world
                        coordinates Generic function to convert
                        N-dimensional grid coordinates to real world
                        coordinates
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
imageGrid               imageGrid
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,ROIVolume-method
                        Get length of 'BrainVector'. This is the numbe
                        rof volumes in the volume vector (e.g. the 4th
                        image dimension)
loadBucket              loadBucket
loadData                Generic function to load data from a data
                        source
loadFSSurface           load Freesurfer ascii surface
loadSurface             load an surface from a set of files
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
mapToColors             mapToColors
matchAnatomy2D          given two named axes return AxisSet2D singleton
matchAnatomy3D          given three named axes return AxisSet3D
                        singleton
matrixToVolumeList      matrixToVolumeList converts a matrix to a list
                        of BrainVolumes with values filled at grid
                        coordinates determined by the 'vox' argument.
mergePartitions         mergePartitions
names,BrainBucketSource-method
                        names
ndim                    Generic function to extract the number of
                        dimensions of an object
neuroim                 neuroim
numClusters             numClusters
origin                  Generic getter to extract image origin
overlay                 overlay two objects
partition               partition
permMat                 Extract permutation matrix
pick                    pick
print                   Generic function to print an object
print,AxisSet2D-method
                        print a 'AxisSet2D' instance
print,AxisSet3D-method
                        print a 'AxisSet3D' instance
print,NamedAxis-method
                        print a 'NamedAxis'
readAFNIHeader          readAFNIHeader
readColumns             Generic function to read a set of column vector
                        from an input source (e.g. 'ColumnReader')
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.
render                  Render an image to create a drawable image.
renderSlice             Render a slice at z coordinate
scaleSeries             Generic functions to scale (center and/or
                        normalize by standard deviation) each series of
                        a 4D image That is, if the 4th dimension is
                        'time' each series is a 1D time series.
series                  Extract vector series from object
seriesIter              seriesIter
show,AxisSet1D-method   show an 'AxisSet1D'
show,AxisSet2D-method   show an 'AxisSet2D'
show,AxisSet3D-method   show an 'AxisSet3D'
show,AxisSet4D-method   show an 'AxisSet4D'
show,BaseMetaInfo-method
                        show a 'BaseMetaInfo'
show,BrainSpace-method
                        show a 'BrainSpace'
show,BrainVector-method
                        show a 'BrainVector'
show,BrainVectorSource-method
                        show a 'BrainVectorSource'
show,BrainVolume-method
                        show a 'BrainVolume'
show,FileMetaInfo-method
                        show a 'FileMetaInfo'
show,NamedAxis-method   show an 'NamedAxis'
show,NullMetaInfo-method
                        show a 'NullMetaInfo'
show,ROIVolume-method   show an 'ROIVolime'
show,SparseBrainVector-method
                        show a 'SparseBrainVector'
show,SurfaceDataMetaInfo-method
                        show an 'SurfaceDataMetaInfo'
show,SurfaceGeometryMetaInfo-method
                        show an 'SurfaceGeometryMetaInfo'
slice                   Extract a 2D slice from an image volume
sliceData               sliceData
space                   Generic function to extract geometric
                        properties of an image.
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 by first splitting by row and then
                        "reducing" by a summary 'function'
splitScale              Generic function to center/scale row-subsets of
                        a matrix or matrix-like object
stripExtension          Generic function to strip extension from file
                        name, given a 'BrainFileDescriptor' instance.
subVector               Generic function to extract a sub-vector from a
                        'BrainVector' object.
takeSeries              Generic function to extract a set of series
                        from a 4D image
takeVolume              Generic function to extract a one or more
                        individual volumes from a four-dimensional
                        image
tesselate               tesselate
trans                   Generic getter to extract image coordinate
                        transformation
values                  Generic function to extract data values of
                        object
voxels                  extract voxel coordinates
writeElements           Generic function to write a sequence of
                        elements from an input source
writeVector             Generic function to write a 4D image vector to
                        disk
writeVolume             Generic function to write a 3D image volume to
                        disk
