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.

Author
Bradley R. Buchsbaum
Date of publication
2016-01-07 23:59:04
Maintainer
Bradley Buchsbaum <brad.buchsbaum@gmail.com>
License
GPL (>= 2)
Version
0.0.6

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