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

Files in this package

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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