# Data Structures and Handling for Neuroimaging Data

## Documentation for package ‘neuroim’ version 0.0.6

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

A B C D E F G H I K L M N O P R S T V W misc

neuroim-package | neuroim

## -- A --

addDim | Generic function to add a dimension to an object
addDim-method | Generic function to add a dimension to an object
AFNIFileDescriptor-class | AFNIFileDescriptor
AFNIMetaInfo | AFNIMetaInfo
AFNIMetaInfo-class | FileMetaInfo
as | conversion from DenseBrainVolume to array
as.array-method | convert 'BrainData' instance to array
as.list-method | as.list
as.logical-method | as.logical
as.mask | Convert to a LogicalBrainVolume
as.mask-method | Convert to a LogicalBrainVolume
as.matrix-method | convert 'BrainData' instance to matrix
as.matrix-method | as.matrix
as.numeric-method | Convert SparseBrainVolume to numeric
as.raster-method | as.raster
as.sparse | Convert to from dense to sparse representation
as.sparse-method | Convert to from dense to sparse representation
as.vector-method | convert 'BrainData' instance to vector
axes | Generic getter function to extract image axes
axes-method | Generic getter function to extract image axes
AxisSet-class | Base
AxisSet1D-class | AxisSet1D
AxisSet2D-class | AxisSet2D
AxisSet3D-class | AxisSet3D
AxisSet4D-class | AxisSet4D
AxisSet5D-class | AxisSet5D
axisToIndex | Generic function to convert 1-dimensional real axis coordinates along a single axis dimension to an 1D index along the same axis
axisToIndex-method | Generic function to convert 1-dimensional real axis coordinates along a single axis dimension to an 1D index along the same axis

## -- B --

Base-class | Base
BaseMetaInfo-class | BaseMetaInfo
BaseSource-class | BaseSource
BinaryReader | BinaryReader
BinaryReader-class | BinaryReader
BinaryWriter | BinaryWriter
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.
bounds | Generic function to extract the spatial bounds (origin + dim * spacing) of an image param x the object
bounds-method | Generic function to extract the spatial bounds (origin + dim * spacing) of an image param x the object
BrainBucket | BrainBucket
BrainBucket-class | BrainBucket
BrainBucketSource | BrainBucketSource
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 | BrainMetaInfo This class contains meta information from an image
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 | BrainSurfaceSource
BrainSurfaceSource-class | BrainSurfaceSource
BrainSurfaceVector-class | BrainSurfaceVector
BrainSurfaceVectorSource-class | BrainSurfaceVectorSource
BrainVector | BrainVector
BrainVector-class | BrainVector
BrainVectorSource | BrainVectorSource
BrainVectorSource-class | BrainVectorSource
BrainVolume | BrainVolume
BrainVolume-class | Base class for image representing 3D volumetric data.
BrainVolumeSource | BrainVolume BrainVolumeSource A class is used to produce a 'BrainVolume' instance
BrainVolumeSource-class | BrainVolume BrainVolumeSource A class is used to produce a 'BrainVolume' instance

## -- C --

close-method | close
clusterCenters | clusterCenters
clusterCenters-method | clusterCenters
ClusteredBrainVolume | ClusteredBrainVolume
ClusteredBrainVolume-class | ClusteredBrainVolume
ColumnReader | ColumnReader
ColumnReader-class | ColumnReader
concat | Concatenate two objects
concat-method | Concatenate two objects
connComp | Find connected components
connComp-method | Find connected components
connComp3D | Extract connected components from a 3D mask
coords | Extract coordinates
coords-method | Extract coordinates
coordToGrid | Generic function to convert N-dimensional real world coordinates to grid coordinates
coordToGrid-method | 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
coordToIndex-method | Generic function to convert N-dimensional real world coordinates to 1D indices

## -- D --

dataFile | Generic function to get the name of the data file, given a file name and a 'BrainFileDescriptor' instance.
dataFile-method | 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
dataFileMatches-method | 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
dataReader-method | Generic function to create data reader
DenseBrainVector | DenseBrainVector
DenseBrainVector-class | DenseBrainVector
DenseBrainVolume | DenseBrainVolume
DenseBrainVolume-class | DenseBrainVolume
dim-method | dim of 'BrainData' object
dim-method | dim
dim-method | dim of 'FileMetaInfo'
dropDim | Generic function to drop a dimension from an object
dropDim-method | Generic function to drop a dimension from an object

## -- E --

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.
eachSeries-method | 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
eachSlice-method | 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
eachVolume-method | Generic function to apply a function to each volume of a four-dimensional image

## -- F --

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
fileMatches-method | 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
FileMetaInfo-class | FileMetaInfo
fill | Generic function to map values from one set to another using a user-supplied lookup table
fill-method | Generic function to map values from one set to another using a user-supplied lookup table
FreesurferAsciiSurfaceFileDescriptor-class | FresurferAsciiSurfaceFileDescriptor
FreesurferSurfaceGeometryMetaInfo-class | FreeSurferSurfaceGeometryMetaInfo This class contains meta information for brain surface geometry

## -- G --

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
gridToCoord-method | 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
gridToIndex-method | Generic function to convert N-dimensional grid coordinate to 1D indices

## -- H --

headerFile | Generic function to get the name of the header file, given a file name and a 'BrainFileDescriptor' instance.
headerFile-method | 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
headerFileMatches-method | Generic function to test whether a file name conforms to the given 'BrainFileDescriptor' instance. Will test for match to header file only

## -- I --

image-method | image
imageGrid | imageGrid
IndexLookupVolume | IndexLookupVolume
IndexLookupVolume-class | IndexLookupVolume
indexToCoord | Generic function to convert 1D indices to N-dimensional real world coordinates
indexToCoord-method | Generic function to convert 1D indices to N-dimensional real world coordinates
indexToGrid | Generic function to convert 1D indices to N-dimensional grid coordinates
indexToGrid-method | Generic function to convert 1D indices to N-dimensional grid coordinates
indices | Extract indices
indices-method | Extract indices
inverseTrans | Generic getter to extract inverse image coordinate transformation
inverseTrans-method | Generic getter to extract inverse image coordinate transformation

## -- K --

Kernel | Create a Kernel object
Kernel-class | Kernel

## -- L --

Layer | Layer
Layer-class | Layer
length-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
loadData-method | 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
LogicalBrainVolume | LogicalBrainVolume
LogicalBrainVolume-class | LogicalBrainVolume
lookup | Index Lookup operation
lookup-method | Index Lookup operation

## -- M --

makeVector | makeVector
makeVolume | makeVolume
map | Generic function to apply a function to an object
map-method | 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
mergePartitions-method | mergePartitions
MNI_SPACE_1MM | MNI SPACE 1MM

## -- N --

NamedAxis-class | NamedAxis
names-method | names
ndim | Generic function to extract the number of dimensions of an object
ndim-method | Generic function to extract the number of dimensions of an object
neuroim | neuroim
NIfTIFileDescriptor-class | NIfTIFileDescriptor
NIfTIMetaInfo | Constructor for 'NIfTIMetaInfo' class
NIfTIMetaInfo-class | FileMetaInfo
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
NullMetaInfo-class | NullMetaInfo
numClusters | numClusters
numClusters-method | numClusters

## -- O --

origin | Generic getter to extract image origin
origin-method | Generic getter to extract image origin
overlay | overlay two objects
overlay-method | overlay two objects

## -- P --

partition | partition
partition-method | partition
permMat | Extract permutation matrix
permMat-method | Extract permutation matrix
pick | pick
print | Generic function to print an object
print-method | print a 'AxisSet2D' instance
print-method | print a 'AxisSet3D' instance
print-method | print a 'NamedAxis'

## -- R --

RandomSearchlight | Create an Random Searchlight iterator
readAFNIHeader | readAFNIHeader
readColumns | Generic function to read a set of column vector from an input source (e.g. 'ColumnReader')
readColumns-method | 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
readElements-method | 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.
readMetaInfo-method | Generic function to read image meta info given a file and a 'BrainFileDescriptor' instance.
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.
render | Render an image to create a drawable image.
render-method | Render an image to create a drawable image.
renderSlice | Render a slice at z coordinate
renderSlice-method | Render a slice at z coordinate
ROIVolume | Create an instance of class ROIVolume
ROIVolume-class | ROIVolume

## -- S --

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.
scaleSeries-method | 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.
Searchlight | Create an exhaustive searchlight iterator
series | Extract vector series from object
series-method | Extract vector series from object
seriesIter | seriesIter
seriesIter-method | seriesIter
show-method | show an 'AxisSet1D'
show-method | show an 'AxisSet2D'
show-method | show an 'AxisSet3D'
show-method | show an 'AxisSet4D'
show-method | show a 'BaseMetaInfo'
show-method | show a 'BrainSpace'
show-method | show a 'BrainVector'
show-method | show a 'BrainVectorSource'
show-method | show a 'BrainVolume'
show-method | show a 'FileMetaInfo'
show-method | show an 'NamedAxis'
show-method | show a 'NullMetaInfo'
show-method | show an 'ROIVolime'
show-method | show a 'SparseBrainVector'
show-method | show an 'SurfaceDataMetaInfo'
show-method | show an 'SurfaceGeometryMetaInfo'
slice | Extract a 2D slice from an image volume
slice-method | Extract a 2D slice from an image volume
sliceData | sliceData
space | Generic function to extract geometric properties of an image.
space-method | Generic function to extract geometric properties of an image.
spacing | Generic function to extract the voxel dimensions of an image
spacing-method | Generic function to extract the voxel dimensions of an image
SparseBrainVector | SparseBrainVector
SparseBrainVector-class | SparseBrainVector
SparseBrainVectorSource | SparseBrainVectorSource
SparseBrainVectorSource-class | SparseBrainVectorSource
SparseBrainVolume | SparseBrainVolume
SparseBrainVolume-class | SparseBrainVolume
splitFill | Generic function to fill disjoint sets of values with the output of a function
splitFill-method | 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'
splitReduce-method | 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
splitScale-method | 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.
stripExtension-method | Generic function to strip extension from file name, given a 'BrainFileDescriptor' instance.
subVector | Generic function to extract a sub-vector from a 'BrainVector' object.
subVector-method | Generic function to extract a sub-vector from a 'BrainVector' object.
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

## -- T --

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
takeVolume-method | Generic function to extract a one or more individual volumes from a four-dimensional image
tesselate | tesselate
tesselate-method | tesselate
trans | Generic getter to extract image coordinate transformation
trans-method | Generic getter to extract image coordinate transformation

## -- V --

values | Generic function to extract data values of object
values-method | Generic function to extract data values of object
voxels | extract voxel coordinates
voxels-method | extract voxel coordinates

## -- W --

writeElements | Generic function to write a sequence of elements from an input source
writeElements-method | Generic function to write a sequence of elements from an input source
writeVector | Generic function to write a 4D image vector to disk
writeVector-method | Generic function to write a 4D image vector to disk
writeVolume | Generic function to write a 3D image volume to disk
writeVolume-method | Generic function to write a 3D image volume to disk

## -- misc --

+-method | overlay two objects
[-method | extract labeled volume from 'BrainBucket'
[-method | extract data from 'ROIVolume'
[-method | extractor
[-method | extractor
[-method | extractor
[-method | extractor
[-method | extractor
[-method | extractor
[-method | extractor
[-method | extractor
[-method | extractor
[[-method | extract labeled volume from 'BrainBucket'