neuroim: Data Structures and Handling for Neuroimaging Data

A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.

AuthorBradley R. Buchsbaum
Date of publication2016-01-07 23:59:04
MaintainerBradley Buchsbaum <brad.buchsbaum@gmail.com>
LicenseGPL (>= 2)
Version0.0.6

View on CRAN

Man pages

addDim-methods: Generic function to add a dimension to an object

AFNIFileDescriptor-class: AFNIFileDescriptor

AFNIMetaInfo-class: AFNIMetaInfo

as.array-BrainData-method: convert 'BrainData' instance to array

as.list-methods: as.list

as.logical-methods: as.logical

as.mask-methods: Convert to a LogicalBrainVolume

as.matrix-BrainData-method: convert 'BrainData' instance to matrix

as.matrix-methods: as.matrix

as-methods: conversion from DenseBrainVolume to array

as.numeric-methods: Convert SparseBrainVolume to numeric

as.raster-methods: as.raster

as.sparse-methods: Convert to from dense to sparse representation

as.vector-BrainData-method: convert 'BrainData' instance to vector

axes-methods: Generic getter function to extract image axes

AxisSet1D-class: AxisSet1D

AxisSet2D-class: AxisSet2D

AxisSet3D-class: AxisSet3D

AxisSet4D-class: AxisSet4D

AxisSet5D-class: AxisSet5D

AxisSet-class: Base

axisToIndex-methods: Generic function to convert 1-dimensional real axis...

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...

bounds-methods: Generic function to extract the spatial bounds (origin + dim...

BrainBucket-class: BrainBucket

BrainBucketSource-class: BrainBucketSource

BrainData-class: BrainData

BrainFileDescriptor-class: BrainFileDescriptor

BrainFileSource-class: BrainFileSource Base class for representing a data source for...

BrainMetaInfo-class: BrainMetaInfo This class contains meta information from an...

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...

close-methods: close

clusterCenters-methods: clusterCenters

ClusteredBrainVolume-class: ClusteredBrainVolume

ColumnReader: ColumnReader

ColumnReader-class: ColumnReader

concat-methods: Concatenate two objects

connComp3D: Extract connected components from a 3D mask

connComp-methods: Find connected components

coords-methods: Extract coordinates

coordToGrid-methods: Generic function to convert N-dimensional real world...

coordToIndex-methods: Generic function to convert N-dimensional real world...

dataFileMatches-methods: Generic function to test whether a file name conforms to the...

dataFile-methods: Generic function to get the name of the data file, given a...

dataReader-methods: Generic function to create data reader

DenseBrainVector-class: DenseBrainVector

DenseBrainVolume-class: DenseBrainVolume

dim-BrainData-method: dim of 'BrainData' object

dim-BrainSpace-method: dim

dim-FileMetaInfo-method: dim of 'FileMetaInfo'

dropDim-methods: Generic function to drop a dimension from an object

eachSeries-methods: Generic functions to apply a function to each series of a 4D...

eachSlice-methods: Generic functions to apply a function to each (2D) slice of...

eachVolume-methods: Generic function to apply a function to each volume of a...

fileMatches-methods: Generic function to test whether a file name conforms to the...

FileMetaInfo-class: FileMetaInfo

fill-methods: Generic function to map values from one set to another using...

FreesurferAsciiSurfaceFileDescriptor-class: FresurferAsciiSurfaceFileDescriptor

FreeSurferSurfaceGeometryMetaInfo-class: FreeSurferSurfaceGeometryMetaInfo This class contains meta...

gridToCoord-methods: Generic function to convert N-dimensional grid coordinate...

gridToIndex-methods: Generic function to convert N-dimensional grid coordinate to...

headerFileMatches-methods: Generic function to test whether a file name conforms to the...

headerFile-methods: Generic function to get the name of the header file, given a...

imageGrid: imageGrid

image-methods: image

IndexLookupVolume-class: IndexLookupVolume

indexToCoord-methods: Generic function to convert 1D indices to N-dimensional real...

indexToGrid-methods: Generic function to convert 1D indices to N-dimensional grid...

indices-methods: Extract indices

internal-methods: .isExtension

inverseTrans-methods: Generic getter to extract inverse image coordinate...

Kernel: Create a Kernel object

Kernel-class: Kernel

Layer: Layer

Layer-class: Layer

length-methods: Get length of 'BrainVector'. This is the numbe rof volumes in...

loadBucket: loadBucket

loadData-methods: 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-class: LogicalBrainVolume

lookup-methods: Index Lookup operation

makeVector: makeVector

makeVolume: makeVolume

map-methods: 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...

mergePartitions-methods: mergePartitions

MNI_SPACE_1MM: MNI SPACE 1MM

NamedAxis-class: NamedAxis

names-methods: names

ndim-methods: Generic function to extract the number of dimensions of an...

neuroim: neuroim

NIfTIFileDescriptor-class: NIfTIFileDescriptor

NIfTIMetaInfo-class: Constructor for 'NIfTIMetaInfo' class

NIMLSurfaceDataMetaInfo: Constructor for 'NIMLSurfaceDataMetaInfo' class

NIMLSurfaceDataMetaInfo-class: NIMLSurfaceDataMetaInfo This class contains meta information...

NIMLSurfaceFileDescriptor-class: NIMLSurfaceFileDescriptor

NullMetaInfo-class: NullMetaInfo

numClusters-methods: numClusters

origin-methods: Generic getter to extract image origin

overlay-methods: overlay two objects

partition-methods: partition

permMat-methods: Extract permutation matrix

pick-methods: pick

print-AxisSet2D-method: print a 'AxisSet2D' instance

print-AxisSet3D-method: print a 'AxisSet3D' instance

print-methods: Generic function to print an object

print-NamedAxis-method: print a 'NamedAxis'

RandomSearchlight: Create an Random Searchlight iterator

readAFNIHeader: readAFNIHeader

readColumns-methods: Generic function to read a set of column vector from an input...

readElements-methods: Generic function to read a sequence of elements from an input...

readHeader: read header information of an image file

readMetaInfo-methods: Generic function to read image meta info given a file and a...

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...

render-methods: Render an image to create a drawable image.

renderSlice-methods: Render a slice at z coordinate

ROIVolume: Create an instance of class ROIVolume

ROIVolume-class: ROIVolume

scaleSeries-methods: Generic functions to scale (center and/or normalize by...

Searchlight: Create an exhaustive searchlight iterator

seriesIter: seriesIter

series-methods: Extract vector series from object

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'

sliceData: sliceData

slice-methods: Extract a 2D slice from an image volume

space-methods: Generic function to extract geometric properties of an image.

spacing-methods: Generic function to extract the voxel dimensions of an image

SparseBrainVector-class: SparseBrainVector

SparseBrainVectorSource-class: SparseBrainVectorSource

SparseBrainVolume-class: SparseBrainVolume

splitFill-methods: Generic function to fill disjoint sets of values with the...

splitReduce-methods: Generic function to summarize subsets of an object by first...

splitScale-methods: Generic function to center/scale row-subsets of a matrix or...

stripExtension-methods: Generic function to strip extension from file name, given a...

sub-BrainBucket-index-missing-ANY-method: extract labeled volume from 'BrainBucket'

sub-ROIVolume-numeric-missing-ANY-method: extract data from 'ROIVolume'

sub-SparseBrainVector-missing-missing-ANY-method: extractor

sub-SparseBrainVector-missing-numeric-ANY-method: extractor

sub-SparseBrainVector-numeric-missing-ANY-method: extractor

sub-SparseBrainVector-numeric-numeric-ANY-method: extractor

sub-SparseBrainVolume-matrix-missing-ANY-method: extractor

sub-SparseBrainVolume-missing-missing-ANY-method: extractor

sub-SparseBrainVolume-missing-numeric-ANY-method: extractor

sub-SparseBrainVolume-numeric-missing-missing-method: extractor

sub-SparseBrainVolume-numeric-numeric-ANY-method: extractor

sub-sub-BrainBucket-index-missing-method: extract labeled volume from 'BrainBucket'

subVector-methods: Generic function to extract a sub-vector from a 'BrainVector'...

SurfaceDataMetaInfo: Constructor for 'SurfaceDataMetaInfo' class

SurfaceDataMetaInfo-class: SurfaceDataMetaInfo This class contains meta information for...

SurfaceGeometryMetaInfo: Constructor for 'SurfaceGeometryMetaInfo' class

SurfaceGeometryMetaInfo-class: SurfaceGeometryMetaInfo This class contains meta information...

takeSeries-methods: Generic function to extract a set of series from a 4D image

takeVolume-methods: Generic function to extract a one or more individual volumes...

tesselate-methods: tesselate

trans-methods: Generic getter to extract image coordinate transformation

values-methods: Generic function to extract data values of object

voxels-methods: extract voxel coordinates

writeElements-methods: Generic function to write a sequence of elements from an...

writeVector-methods: Generic function to write a 4D image vector to disk

writeVolume-methods: Generic function to write a 3D image volume to disk

Functions

addDim Man page
addDim,BrainSpace,numeric-method Man page
AFNIFileDescriptor-class Man page
AFNIMetaInfo Man page
AFNIMetaInfo-class Man page
as Man page
as.array,BrainData-method Man page
as.list,BrainVector-method Man page
as.list,SparseBrainVector-method Man page
as.logical,BrainVolume-method Man page
as.mask Man page
as.mask,BrainVolume,missing-method Man page
as.mask,BrainVolume,numeric-method Man page
as.matrix,BrainData-method Man page
as.matrix,DenseBrainVector-method Man page
as.matrix,SparseBrainVector-method Man page
as.numeric,SparseBrainVolume-method Man page
as.raster,Layer-method Man page
as.sparse Man page
as.sparse,DenseBrainVector,LogicalBrainVolume-method Man page
as.sparse,DenseBrainVector,numeric-method Man page
as.sparse,DenseBrainVolume,LogicalBrainVolume-method Man page
as.sparse,DenseBrainVolume,numeric-method Man page
as.vector,BrainData-method Man page
axes Man page
axes,BrainData-method Man page
axes,BrainSpace-method Man page
AxisSet1D-class Man page
AxisSet2D-class Man page
AxisSet3D-class Man page
AxisSet4D-class Man page
AxisSet5D-class Man page
AxisSet-class Man page
axisToIndex Man page
axisToIndex,BrainSpace,numeric,numeric-method Man page
Base-class Man page
BaseMetaInfo-class Man page
BaseSource-class Man page
BinaryReader Man page
BinaryReader-class Man page
BinaryWriter Man page
BinaryWriter-class Man page
BootstrapSearchlight Man page
bounds Man page
bounds,BrainData-method Man page
bounds,BrainSpace-method Man page
BrainBucket Man page
BrainBucket-class Man page
[,BrainBucket,index,missing,ANY-method Man page
[[,BrainBucket,index,missing-method Man page
BrainBucketSource Man page
BrainBucketSource-class Man page
BrainData-class Man page
BrainFileDescriptor-class Man page
BrainFileSource-class Man page
BrainMetaInfo Man page
BrainMetaInfo-class Man page
BrainSlice Man page
BrainSlice-class Man page
BrainSource-class Man page
BrainSpace Man page
BrainSpace-class Man page
BrainSurface-class Man page
BrainSurfaceSource Man page
BrainSurfaceSource-class Man page
BrainSurfaceVector-class Man page
BrainSurfaceVectorSource-class Man page
BrainVector Man page
BrainVector-class Man page
BrainVectorSource Man page
BrainVectorSource-class Man page
BrainVolume Man page
BrainVolume-class Man page
BrainVolumeSource Man page
BrainVolumeSource-class Man page
close,BinaryReader-method Man page
close,BinaryWriter-method Man page
clusterCenters Man page
clusterCenters,ClusteredBrainVolume,matrix,missing-method Man page
ClusteredBrainVolume Man page
ClusteredBrainVolume-class Man page
ColumnReader Man page
ColumnReader-class Man page
concat Man page
.concat4D Man page
concat,BrainVector,BrainVector-method Man page
concat,BrainVector,BrainVolume-method Man page
concat,BrainVolume,BrainVector-method Man page
concat,DenseBrainVolume,DenseBrainVolume-method Man page
concat,SparseBrainVector,SparseBrainVector-method Man page
connComp Man page
connComp3D Man page
connComp,BrainVolume-method Man page
coords Man page
coords,IndexLookupVolume-method Man page
coords,ROIVolume-method Man page
coords,SparseBrainVector-method Man page
coordToGrid Man page
coordToGrid,BrainSpace,matrix-method Man page
coordToGrid,BrainSpace,numeric-method Man page
coordToGrid,BrainVolume,matrix-method Man page
coordToIndex Man page
coordToIndex,BrainSpace,matrix-method Man page
coordToIndex,BrainSpace,numeric-method Man page
coordToIndex,BrainVolume,matrix-method Man page
dataFile Man page
dataFile,BrainFileDescriptor,character-method Man page
dataFileMatches Man page
dataFileMatches,BrainFileDescriptor,character-method Man page
dataReader Man page
dataReader,AFNIMetaInfo-method Man page
dataReader,NIfTIMetaInfo-method Man page
dataReader,NIMLSurfaceDataMetaInfo-method Man page
DenseBrainVector Man page
DenseBrainVector-class Man page
DenseBrainVolume Man page
DenseBrainVolume-class Man page
dim,BrainData-method Man page
dim,BrainSpace-method Man page
dim,FileMetaInfo-method Man page
dropDim Man page
dropDim,AxisSet2D,missing-method Man page
dropDim,AxisSet2D,numeric-method Man page
dropDim,AxisSet3D,missing-method Man page
dropDim,AxisSet3D,numeric-method Man page
dropDim,BrainSpace,missing-method Man page
dropDim,BrainSpace,numeric-method Man page
eachSeries Man page
eachSeries,BrainVector,function,missing-method Man page
eachSeries,SparseBrainVector,function,logical-method Man page
eachSlice Man page
eachSlice,BrainVolume,function,logical-method Man page
eachSlice,BrainVolume,function,missing-method Man page
eachVolume Man page
eachVolume,BrainBucket,function,logical,ANY-method Man page
eachVolume,BrainBucket,function,missing,missing-method Man page
eachVolume,BrainVector,function,logical,ANY-method Man page
eachVolume,BrainVector,function,missing,BrainVolume-method Man page
eachVolume,BrainVector,function,missing,missing-method Man page
eachVolume,SparseBrainVector,function,logical,missing-method Man page
eachVolume,SparseBrainVector,function,missing,LogicalBrainVolume Man page
eachVolume,SparseBrainVector,function,missing,missing-method Man page
.extract.array Man page
fileMatches Man page
fileMatches,BrainFileDescriptor,character-method Man page
FileMetaInfo-class Man page
fill Man page
fill,BrainVolume,list-method Man page
fill,BrainVolume,matrix-method Man page
FreesurferAsciiSurfaceFileDescriptor-class Man page
FreesurferSurfaceGeometryMetaInfo-class Man page
.getDataCode Man page
.getDataSize Man page
.getDataStorage Man page
.getEndian Man page
.getRStorage Man page
gridToCoord Man page
gridToCoord,BrainSpace,matrix-method Man page
gridToCoord,BrainVolume,matrix-method Man page
gridToIndex Man page
.gridToIndex Man page
.gridToIndex3D Man page
gridToIndex,BrainSlice,matrix-method Man page
gridToIndex,BrainSpace,matrix-method Man page
gridToIndex,BrainSpace,numeric-method Man page
gridToIndex,BrainVolume,matrix-method Man page
gridToIndex,BrainVolume,numeric-method Man page
headerFile Man page
headerFile,BrainFileDescriptor,character-method Man page
headerFileMatches Man page
headerFileMatches,BrainFileDescriptor,character-method Man page
image,BrainVolume-method Man page
imageGrid Man page
image,Layer-method Man page
image,Overlay-method Man page
IndexLookupVolume Man page
IndexLookupVolume-class Man page
indexToCoord Man page
indexToCoord,BrainSpace,index-method Man page
indexToCoord,BrainVolume,index-method Man page
indexToGrid Man page
.indexToGrid Man page
indexToGrid,BrainSlice,index-method Man page
indexToGrid,BrainSpace,index-method Man page
indexToGrid,BrainVector,index-method Man page
indexToGrid,BrainVolume,index-method Man page
indices Man page
indices,IndexLookupVolume-method Man page
indices,ROIVolume-method Man page
indices,SparseBrainVector-method Man page
inverseTrans Man page
inverseTrans,BrainData-method Man page
inverseTrans,BrainSpace-method Man page
.isExtension Man page
Kernel Man page
Kernel-class Man page
Layer Man page
Layer-class Man page
+,Layer,Layer-method Man page
length,BrainVector-method Man page
length,ROIVolume-method Man page
loadBucket Man page
loadData Man page
loadData,BrainBucketSource-method Man page
loadData,BrainSurfaceSource-method Man page
loadData,BrainVectorSource-method Man page
loadData,BrainVolumeSource-method Man page
loadData,SparseBrainVectorSource-method Man page
loadFSSurface Man page
loadSurface Man page
loadVector Man page
loadVolume Man page
loadVolumeList Man page
LogicalBrainVolume Man page
LogicalBrainVolume-class Man page
lookup Man page
lookup,IndexLookupVolume,numeric-method Man page
lookup,SparseBrainVector,numeric-method Man page
makeVector Man page
makeVolume Man page
map Man page
map,BrainVolume,Kernel-method Man page
mapToColors Man page
matchAnatomy2D Man page
matchAnatomy3D Man page
.matrixToQuatern Man page
matrixToVolumeList Man page
mergePartitions Man page
mergePartitions,ClusteredBrainVolume,numeric,matrix-method Man page
MNI_SPACE_1MM Man page
NamedAxis-class Man page
names,BrainBucket-method Man page
names,BrainBucketSource-method Man page
ndim Man page
ndim,AxisSet-method Man page
ndim,BrainData-method Man page
ndim,BrainSpace-method Man page
neuroim Man page
neuroim-package Man page
.niftiExt Man page
NIfTIFileDescriptor-class Man page
NIfTIMetaInfo Man page
NIfTIMetaInfo-class Man page
NIMLSurfaceDataMetaInfo Man page
NIMLSurfaceDataMetaInfo-class Man page
NIMLSurfaceFileDescriptor-class Man page
NullMetaInfo-class Man page
numClusters Man page
numClusters,ClusteredBrainVolume-method Man page
origin Man page
origin,BrainData-method Man page
origin,BrainSpace-method Man page
overlay Man page
overlay,Layer,Layer-method Man page
+,Overlay,Layer-method Man page
partition Man page
partition,ClusteredBrainVolume,numeric,matrix-method Man page
permMat Man page
permMat,AxisSet2D-method Man page
pick Man page
print Man page
print,AxisSet2D-method Man page
print,AxisSet3D-method Man page
print,NamedAxis-method Man page
RandomSearchlight Man page
readAFNIHeader Man page
readColumns Man page
readColumns,ColumnReader,numeric-method Man page
readElements Man page
readElements,BinaryReader,numeric-method Man page
readHeader Man page
readMetaInfo Man page
readMetaInfo,AFNIFileDescriptor-method Man page
readMetaInfo,FreesurferAsciiSurfaceFileDescriptor-method Man page
readMetaInfo,NIfTIFileDescriptor-method Man page
readMetaInfo,NIMLSurfaceFileDescriptor-method Man page
RegionCube Man page
RegionSphere Man page
RegionSquare Man page
render Man page
render,BrainSlice,numeric,numeric,character-method Man page
renderSlice Man page
renderSlice,Layer,numeric,numeric,numeric,missing-method Man page
renderSlice,Overlay,numeric,numeric,numeric,missing-method Man page
ROIVolume Man page
ROIVolume-class Man page
[,ROIVolume,numeric,missing,ANY-method Man page
scaleSeries Man page
scaleSeries,BrainVector,logical,logical-method Man page
scaleSeries,BrainVector,logical,missing-method Man page
scaleSeries,BrainVector,missing,logical-method Man page
scaleSeries,BrainVector,missing,missing-method Man page
Searchlight Man page
series Man page
series,BrainVector,matrix-method Man page
series,BrainVector,numeric-method Man page
seriesIter Man page
seriesIter,BrainVector-method Man page
seriesIter,SparseBrainVector-method Man page
series,SparseBrainVector,matrix-method Man page
series,SparseBrainVector,numeric-method Man page
show,AxisSet1D-method Man page
show,AxisSet2D-method Man page
show,AxisSet3D-method Man page
show,AxisSet4D-method Man page
show,BaseMetaInfo-method Man page
show,BrainSpace-method Man page
show,BrainVector-method Man page
show,BrainVectorSource-method Man page
show,BrainVolume-method Man page
show,FileMetaInfo-method Man page
show,NamedAxis-method Man page
show,NullMetaInfo-method Man page
show,ROIVolume-method Man page
show,SparseBrainVector-method Man page
show,SurfaceDataMetaInfo-method Man page
show,SurfaceGeometryMetaInfo-method Man page
slice Man page
slice,BrainVolume,numeric,numeric,character-method Man page
sliceData Man page
space Man page
space,BrainData-method Man page
space,BrainSpace-method Man page
space,IndexLookupVolume-method Man page
spacing Man page
spacing,BrainData-method Man page
spacing,BrainSpace-method Man page
SparseBrainVector Man page
SparseBrainVector-class Man page
[,SparseBrainVector,missing,missing,ANY-method Man page
[,SparseBrainVector,missing,numeric,ANY-method Man page
[,SparseBrainVector,numeric,missing,ANY-method Man page
[,SparseBrainVector,numeric,numeric,ANY-method Man page
SparseBrainVectorSource Man page
SparseBrainVectorSource-class Man page
SparseBrainVolume Man page
SparseBrainVolume-class Man page
[,SparseBrainVolume,matrix,missing,ANY-method Man page
[,SparseBrainVolume,missing,missing,ANY-method Man page
[,SparseBrainVolume,missing,numeric,ANY-method Man page
[,SparseBrainVolume,numeric,missing,missing-method Man page
[,SparseBrainVolume,numeric,numeric,ANY-method Man page
splitFill Man page
splitFill,BrainVolume,factor,function-method Man page
splitReduce Man page
splitReduce,BrainVector,factor,function-method Man page
splitReduce,BrainVector,factor,missing-method Man page
splitReduce,matrix,factor,function-method Man page
splitReduce,matrix,factor,missing-method Man page
splitReduce,matrix,integer,function-method Man page
splitReduce,matrix,integer,missing-method Man page
splitScale Man page
splitScale,matrix,factor,logical,logical-method Man page
splitScale,matrix,factor,missing,missing-method Man page
stripExtension Man page
stripExtension,BrainFileDescriptor,character-method Man page
subVector Man page
subVector,DenseBrainVector,numeric-method Man page
subVector,SparseBrainVector,numeric-method Man page
SurfaceDataMetaInfo Man page
SurfaceDataMetaInfo-class Man page
SurfaceGeometryMetaInfo Man page
SurfaceGeometryMetaInfo-class Man page
takeSeries Man page
takeVolume Man page
takeVolume,BrainVector,numeric-method Man page
takeVolume,SparseBrainVector,numeric-method Man page
tesselate Man page
tesselate,LogicalBrainVolume,numeric-method Man page
trans Man page
trans,BrainData-method Man page
trans,BrainMetaInfo-method Man page
trans,BrainSpace-method Man page
trans,NIfTIMetaInfo-method Man page
values Man page
values,ROIVolume-method Man page
voxels Man page
voxels,Kernel-method Man page
writeElements Man page
writeElements,BinaryWriter,numeric-method Man page
writeVector Man page
writeVector,BrainVector,character,character,missing-method Man page
writeVector,BrainVector,character,missing,character,ANY-method Man page
writeVector,BrainVector,character,missing,character-method Man page
writeVector,BrainVector,character,missing,missing-method Man page
writeVolume Man page
writeVolume,BrainVolume,character,character,missing-method Man page
writeVolume,BrainVolume,character,missing,character-method Man page
writeVolume,BrainVolume,character,missing,missing-method Man page
writeVolume,ClusteredBrainVolume,character,missing,missing-metho Man page

Files

neuroim
neuroim/inst
neuroim/inst/tests
neuroim/inst/tests/test-indices.R
neuroim/inst/extdata
neuroim/inst/extdata/global_mask.nii
neuroim/inst/doc
neuroim/inst/doc/regionOfInterest.R
neuroim/inst/doc/neuroim.Rmd
neuroim/inst/doc/neuroim.html
neuroim/inst/doc/regionOfInterest.Rmd
neuroim/inst/doc/FileIO.R
neuroim/inst/doc/regionOfInterest.html
neuroim/inst/doc/FileIO.html
neuroim/inst/doc/FileIO.Rmd
neuroim/inst/doc/neuroim.R
neuroim/tests
neuroim/tests/runit-connComp3D.R
neuroim/tests/runit-BrainVector.R
neuroim/tests/runit-filtertest.R
neuroim/tests/runit-BrainBucket.R
neuroim/tests/runit-BrainMetaInfo.R
neuroim/tests/testthat
neuroim/tests/testthat/test-roivolume.R
neuroim/tests/test-all.R
neuroim/tests/runit-BrainVolume.R
neuroim/src
neuroim/src/indexFuns.cpp
neuroim/src/RcppExports.cpp
neuroim/NAMESPACE
neuroim/data
neuroim/data/MNI_SPACE_1MM.RData
neuroim/R
neuroim/R/Display.R neuroim/R/BrainRegion3D.R neuroim/R/BrainFileDescriptor.R neuroim/R/SparseBrainVector.R neuroim/R/FREESURFER_IO.R neuroim/R/BrainMetaInfo.R neuroim/R/AllClass.R neuroim/R/conncomp.R neuroim/R/BrainSpace.R neuroim/R/BrainData.R neuroim/R/NIFTI_IO.R neuroim/R/BrainVector.R neuroim/R/common.R neuroim/R/BrainSlice.R neuroim/R/BrainVolume.R neuroim/R/RcppExports.R neuroim/R/datadoc.R neuroim/R/BinaryIO.R neuroim/R/AFNI_IO.R neuroim/R/Axis.R neuroim/R/AllGeneric.R neuroim/R/BrainSurface.R neuroim/R/Ops.R neuroim/R/neuroim.R neuroim/R/IndexLookupVolume.R
neuroim/vignettes
neuroim/vignettes/neuroim.Rmd
neuroim/vignettes/regionOfInterest.Rmd
neuroim/vignettes/FileIO.Rmd
neuroim/MD5
neuroim/build
neuroim/build/vignette.rds
neuroim/DESCRIPTION
neuroim/man
neuroim/man/as.matrix-BrainData-method.Rd neuroim/man/as.vector-BrainData-method.Rd neuroim/man/as-methods.Rd neuroim/man/loadBucket.Rd neuroim/man/makeVolume.Rd neuroim/man/loadVector.Rd neuroim/man/stripExtension-methods.Rd neuroim/man/BrainVectorSource-class.Rd neuroim/man/sub-SparseBrainVolume-missing-missing-ANY-method.Rd neuroim/man/ColumnReader-class.Rd neuroim/man/splitReduce-methods.Rd neuroim/man/as.sparse-methods.Rd neuroim/man/as.logical-methods.Rd neuroim/man/renderSlice-methods.Rd neuroim/man/BrainSlice.Rd neuroim/man/writeElements-methods.Rd neuroim/man/RegionCube.Rd neuroim/man/BrainSurfaceVector-class.Rd neuroim/man/sub-SparseBrainVector-missing-missing-ANY-method.Rd neuroim/man/BrainBucketSource-class.Rd neuroim/man/eachVolume-methods.Rd neuroim/man/show-AxisSet3D-method.Rd neuroim/man/show-AxisSet1D-method.Rd neuroim/man/tesselate-methods.Rd neuroim/man/ROIVolume-class.Rd neuroim/man/dim-BrainSpace-method.Rd neuroim/man/bounds-methods.Rd neuroim/man/Searchlight.Rd neuroim/man/loadFSSurface.Rd neuroim/man/LogicalBrainVolume-class.Rd neuroim/man/AxisSet1D-class.Rd neuroim/man/AFNIFileDescriptor-class.Rd neuroim/man/takeVolume-methods.Rd neuroim/man/BrainSurfaceSource-class.Rd neuroim/man/dropDim-methods.Rd neuroim/man/ColumnReader.Rd neuroim/man/readMetaInfo-methods.Rd neuroim/man/close-methods.Rd neuroim/man/ClusteredBrainVolume-class.Rd neuroim/man/splitScale-methods.Rd neuroim/man/clusterCenters-methods.Rd neuroim/man/headerFile-methods.Rd neuroim/man/subVector-methods.Rd neuroim/man/BrainBucket-class.Rd neuroim/man/SparseBrainVector-class.Rd neuroim/man/sub-ROIVolume-numeric-missing-ANY-method.Rd neuroim/man/takeSeries-methods.Rd neuroim/man/as.numeric-methods.Rd neuroim/man/BrainSurfaceVectorSource-class.Rd neuroim/man/fill-methods.Rd neuroim/man/FreeSurferSurfaceGeometryMetaInfo-class.Rd neuroim/man/show-SparseBrainVector-method.Rd neuroim/man/series-methods.Rd neuroim/man/Layer.Rd neuroim/man/BrainSurface-class.Rd neuroim/man/numClusters-methods.Rd neuroim/man/matrixToVolumeList.Rd neuroim/man/gridToCoord-methods.Rd neuroim/man/FileMetaInfo-class.Rd neuroim/man/ndim-methods.Rd neuroim/man/permMat-methods.Rd neuroim/man/as.raster-methods.Rd neuroim/man/space-methods.Rd neuroim/man/BrainFileSource-class.Rd neuroim/man/length-methods.Rd neuroim/man/as.array-BrainData-method.Rd neuroim/man/pick-methods.Rd neuroim/man/show-NamedAxis-method.Rd neuroim/man/names-methods.Rd neuroim/man/makeVector.Rd neuroim/man/print-AxisSet3D-method.Rd neuroim/man/spacing-methods.Rd neuroim/man/dataFile-methods.Rd neuroim/man/connComp3D.Rd neuroim/man/as.matrix-methods.Rd neuroim/man/NIMLSurfaceDataMetaInfo-class.Rd neuroim/man/NIMLSurfaceDataMetaInfo.Rd neuroim/man/sub-SparseBrainVector-missing-numeric-ANY-method.Rd neuroim/man/SurfaceDataMetaInfo.Rd neuroim/man/Base-class.Rd neuroim/man/as.mask-methods.Rd neuroim/man/gridToIndex-methods.Rd neuroim/man/internal-methods.Rd neuroim/man/AFNIMetaInfo-class.Rd neuroim/man/axes-methods.Rd neuroim/man/render-methods.Rd neuroim/man/indexToCoord-methods.Rd neuroim/man/neuroim.Rd neuroim/man/BaseSource-class.Rd neuroim/man/AxisSet4D-class.Rd neuroim/man/SurfaceGeometryMetaInfo-class.Rd neuroim/man/BrainVolume-class.Rd neuroim/man/trans-methods.Rd neuroim/man/indexToGrid-methods.Rd neuroim/man/image-methods.Rd neuroim/man/readAFNIHeader.Rd neuroim/man/DenseBrainVolume-class.Rd neuroim/man/BrainVolume.Rd neuroim/man/show-BrainVolume-method.Rd neuroim/man/coordToGrid-methods.Rd neuroim/man/sub-SparseBrainVolume-numeric-missing-missing-method.Rd neuroim/man/show-SurfaceGeometryMetaInfo-method.Rd neuroim/man/NullMetaInfo-class.Rd neuroim/man/sub-SparseBrainVector-numeric-missing-ANY-method.Rd neuroim/man/mergePartitions-methods.Rd neuroim/man/addDim-methods.Rd neuroim/man/RegionSphere.Rd neuroim/man/indices-methods.Rd neuroim/man/mapToColors.Rd neuroim/man/BrainSource-class.Rd neuroim/man/AxisSet-class.Rd neuroim/man/SurfaceGeometryMetaInfo.Rd neuroim/man/eachSlice-methods.Rd neuroim/man/BrainFileDescriptor-class.Rd neuroim/man/writeVector-methods.Rd neuroim/man/SurfaceDataMetaInfo-class.Rd neuroim/man/sub-SparseBrainVolume-numeric-numeric-ANY-method.Rd neuroim/man/show-BaseMetaInfo-method.Rd neuroim/man/DenseBrainVector-class.Rd neuroim/man/matchAnatomy2D.Rd neuroim/man/sub-SparseBrainVolume-matrix-missing-ANY-method.Rd neuroim/man/BootstrapSearchlight.Rd neuroim/man/eachSeries-methods.Rd neuroim/man/NamedAxis-class.Rd neuroim/man/RegionSquare.Rd neuroim/man/AxisSet5D-class.Rd neuroim/man/AxisSet3D-class.Rd neuroim/man/show-BrainVector-method.Rd neuroim/man/sub-sub-BrainBucket-index-missing-method.Rd neuroim/man/NIMLSurfaceFileDescriptor-class.Rd neuroim/man/loadData-methods.Rd neuroim/man/dataReader-methods.Rd neuroim/man/show-AxisSet4D-method.Rd neuroim/man/axisToIndex-methods.Rd neuroim/man/lookup-methods.Rd neuroim/man/connComp-methods.Rd neuroim/man/SparseBrainVolume-class.Rd neuroim/man/print-methods.Rd neuroim/man/sub-BrainBucket-index-missing-ANY-method.Rd neuroim/man/RandomSearchlight.Rd neuroim/man/seriesIter.Rd neuroim/man/NIfTIFileDescriptor-class.Rd neuroim/man/sub-SparseBrainVector-numeric-numeric-ANY-method.Rd neuroim/man/BrainMetaInfo-class.Rd neuroim/man/BrainVector-class.Rd neuroim/man/as.list-methods.Rd neuroim/man/readColumns-methods.Rd neuroim/man/BrainVectorSource.Rd neuroim/man/show-BrainSpace-method.Rd neuroim/man/concat-methods.Rd neuroim/man/fileMatches-methods.Rd neuroim/man/show-SurfaceDataMetaInfo-method.Rd neuroim/man/values-methods.Rd neuroim/man/readHeader.Rd neuroim/man/BrainVolumeSource-class.Rd neuroim/man/dataFileMatches-methods.Rd neuroim/man/show-BrainVectorSource-method.Rd neuroim/man/slice-methods.Rd neuroim/man/writeVolume-methods.Rd neuroim/man/imageGrid.Rd neuroim/man/loadSurface.Rd neuroim/man/FreesurferAsciiSurfaceFileDescriptor-class.Rd neuroim/man/BinaryReader.Rd neuroim/man/sub-SparseBrainVolume-missing-numeric-ANY-method.Rd neuroim/man/print-NamedAxis-method.Rd neuroim/man/sliceData.Rd neuroim/man/BaseMetaInfo-class.Rd neuroim/man/partition-methods.Rd neuroim/man/scaleSeries-methods.Rd neuroim/man/dim-BrainData-method.Rd neuroim/man/Kernel.Rd neuroim/man/loadVolume.Rd neuroim/man/BrainSpace.Rd neuroim/man/show-FileMetaInfo-method.Rd neuroim/man/BinaryWriter-class.Rd neuroim/man/matchAnatomy3D.Rd neuroim/man/show-NullMetaInfo-method.Rd neuroim/man/coordToIndex-methods.Rd neuroim/man/ROIVolume.Rd neuroim/man/voxels-methods.Rd neuroim/man/loadVolumeList.Rd neuroim/man/BrainSpace-class.Rd neuroim/man/MNI_SPACE_1MM.Rd neuroim/man/splitFill-methods.Rd neuroim/man/print-AxisSet2D-method.Rd neuroim/man/show-AxisSet2D-method.Rd neuroim/man/headerFileMatches-methods.Rd neuroim/man/SparseBrainVectorSource-class.Rd neuroim/man/overlay-methods.Rd neuroim/man/dim-FileMetaInfo-method.Rd neuroim/man/Layer-class.Rd neuroim/man/BrainSlice-class.Rd neuroim/man/NIfTIMetaInfo-class.Rd neuroim/man/coords-methods.Rd neuroim/man/BinaryReader-class.Rd neuroim/man/readElements-methods.Rd neuroim/man/BrainData-class.Rd neuroim/man/inverseTrans-methods.Rd neuroim/man/map-methods.Rd neuroim/man/Kernel-class.Rd neuroim/man/AxisSet2D-class.Rd neuroim/man/show-ROIVolume-method.Rd neuroim/man/origin-methods.Rd neuroim/man/IndexLookupVolume-class.Rd

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