Data Structures and Handling for Neuroimaging Data
Generic function to write a 4D image vector to disk
given three named axes return AxisSet3D singleton
matrixToVolumeList converts a matrix to a list of BrainVolumes with va...
mergePartitions
NamedAxis
names
Generic function to extract the number of dimensions of an object
neuroim
NIfTIFileDescriptor
Constructor for NIfTIMetaInfo class
NIMLSurfaceDataMetaInfoThis class contains meta information for surfac...
Constructor for NIMLSurfaceDataMetaInfo class
NIMLSurfaceFileDescriptor
NullMetaInfo
numClusters
Generic getter to extract image origin
overlay two objects
partition
Extract permutation matrix
pick
print a AxisSet2D instance
print a AxisSet3D instance
Generic function to print an object
print a NamedAxis
Create an Random Searchlight iterator
readAFNIHeader
Generic function to read a set of column vector from an input source (...
Generic function to read a sequence of elements from an input source
read header information of an image file
Generic function to read image meta info given a file and a `BrainFile...
Create A Cuboid Region of Interest
Create A Spherical Region of Interest
Generic function to extract a one or more individual volumes from a fo...
tesselate
Generic getter to extract image coordinate transformation
Generic function to extract data values of object
extract voxel coordinates
Generic function to write a sequence of elements from an input source
Create a square region of interest where the z-dimension is fixed at o...
Render an image to create a drawable image.
Render a slice at z coordinate
ROIVolume
Create an instance of class ROIVolume
Generic functions to scale (center and/or normalize by standard deviat...
Create an exhaustive searchlight iterator
Extract vector series from object
seriesIter
show an AxisSet1D
show an AxisSet2D
show an AxisSet3D
show an AxisSet4D
show a BaseMetaInfo
show a BrainSpace
show a BrainVector
show a BrainVectorSource
show a BrainVolume
show a FileMetaInfo
show an NamedAxis
show a NullMetaInfo
show an ROIVolime
show a SparseBrainVector
show an SurfaceDataMetaInfo
show an SurfaceGeometryMetaInfo
Extract a 2D slice from an image volume
sliceData
Generic function to extract geometric properties of an image.
Generic function to extract the voxel dimensions of an image
SparseBrainVector
SparseBrainVectorSource
SparseBrainVolume
Generic function to fill disjoint sets of values with the output of a ...
Generic function to summarize subsets of an object by first splitting ...
Generic function to center/scale row-subsets of a matrix or matrix-lik...
Generic function to strip extension from file name, given a `BrainFile...
extract labeled volume from BrainBucket
extract data from ROIVolume
extractor
extractor
extractor
extractor
extractor
extractor
extractor
extractor
extractor
extract labeled volume from BrainBucket
Generic function to extract a sub-vector from a BrainVector object.
SurfaceDataMetaInfoThis class contains meta information for surface-ba...
Constructor for SurfaceDataMetaInfo class
SurfaceGeometryMetaInfoThis class contains meta information for brain ...
Constructor for SurfaceGeometryMetaInfo class
Generic function to extract a set of series from a 4D image
Generic function to add a dimension to an object
AFNIFileDescriptor
AFNIMetaInfo
conversion from DenseBrainVolume to array
convert BrainData instance to array
as.list
as.logical
Convert to a LogicalBrainVolume
convert BrainData instance to matrix
as.matrix
Convert SparseBrainVolume to numeric
as.raster
Convert to from dense to sparse representation
convert BrainData instance to vector
Generic getter function to extract image axes
Base
AxisSet1D
AxisSet2D
AxisSet3D
AxisSet4D
AxisSet5D
Generic function to convert 1-dimensional real axis coordinates along ...
Base
BaseMetaInfo
BaseSource
BinaryReader
BinaryReader
BinaryWriter
Create a searchlight iterator that samples regions from within a mask....
Generic function to extract the spatial bounds (origin + dim * spacing...
BrainBucket
BrainBucketSource
BrainData
BrainFileDescriptor
BrainFileSourceBase class for representing a data source for images. T...
BrainMetaInfoThis class contains meta information from an image
BrainSlice
BrainSlice constructor
BrainSource
BrainSpace
Constructor function for BrainSpace class
BrainSurface
BrainSurfaceSource
BrainSurfaceVector
BrainSurfaceVectorSource
BrainVector
BrainVectorSource
BrainVectorSource
Base class for image representing 3D volumetric data.
BrainVolume
BrainVolume BrainVolumeSourceA class is used to produce a `BrainVolume...
close
clusterCenters
ClusteredBrainVolume
ColumnReader
ColumnReader
Concatenate two objects
Find connected components
Extract connected components from a 3D mask
Extract coordinates
Generic function to convert N-dimensional real world coordinates to gr...
Generic function to convert N-dimensional real world coordinates to 1D...
Generic function to get the name of the data file, given a file name a...
Generic function to test whether a file name conforms to the given a `...
Generic function to create data reader
DenseBrainVector
DenseBrainVolume
dim of BrainData object
dim
dim of FileMetaInfo
Generic function to drop a dimension from an object
Generic functions to apply a function to each series of a 4D image Tha...
Generic functions to apply a function to each (2D) slice of an image
Generic function to apply a function to each volume of a four-dimensio...
Generic function to test whether a file name conforms to the given `Br...
FileMetaInfo
Generic function to map values from one set to another using a user-su...
FresurferAsciiSurfaceFileDescriptor
FreeSurferSurfaceGeometryMetaInfoThis class contains meta information ...
Generic function to convert N-dimensional grid coordinate coordinates ...
Generic function to convert N-dimensional grid coordinate to 1D indice...
Generic function to get the name of the header file, given a file name...
Generic function to test whether a file name conforms to the given `Br...
image
imageGrid
IndexLookupVolume
Generic function to convert 1D indices to N-dimensional real world coo...
Generic function to convert 1D indices to N-dimensional grid coordinat...
Extract indices
.isExtension
Generic getter to extract inverse image coordinate transformation
Kernel
Create a Kernel object
Layer
Layer
Get length of BrainVector. This is the numbe rof volumes in the volu...
loadBucket
Generic function to load data from a data source
load Freesurfer ascii surface
load an surface from a set of files
loadVector
Load an image volume from a file
loadVolList
LogicalBrainVolume
Index Lookup operation
makeVector
makeVolume
Generic function to apply a function to an object
mapToColors
given two named axes return AxisSet2D singleton
Generic function to write a 3D image volume to disk
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.