Data Structures and Handling for Neuroimaging Data

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Documentation for package ‘neuroim’ version 0.0.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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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'