Generic function to extract the spatial bounds (origin + dim * spacing) of an image
param x the object
Constructor for NIMLSurfaceDataMetaInfo
class
IndexLookupVolume
BaseMetaInfo
BinaryReader
AFNIFileDescriptor
BaseSource
NullMetaInfo
AFNIMetaInfo
FileMetaInfo
AxisSet3D
Base
BinaryReader
FreesurferSurfaceGeometryMetaInfo-class
FreeSurferSurfaceGeometryMetaInfo
This class contains meta information for brain surface geometry
Constructor function for BrainSpace
class
Base
ROIVolume
AxisSet1D
BrainSurfaceVector
BrainVolume
BrainVolumeSource
A class is used to produce a BrainVolume
instance
DenseBrainVector
AxisSet5D
FreesurferAsciiSurfaceFileDescriptor-class
FresurferAsciiSurfaceFileDescriptor
BrainSpace
BrainVectorSource
Generic function to drop a dimension from an object
Generic function to convert N-dimensional real world coordinates to 1D indices
loadVolList
BrainSlice
show a NullMetaInfo
Generic getter to extract image origin
Generic function to load data from a data source
ColumnReader
readAFNIHeader
Layer
ClusteredBrainVolume-class
ClusteredBrainVolume
AxisSet4D
Generic function to add a dimension to an object
close,BinaryReader-method
close
mergePartitions
BrainData
Create an Random Searchlight iterator
Create a Kernel object
Create an instance of class ROIVolume
BrainSurfaceVectorSource-class
BrainSurfaceVectorSource
BrainBucketSource
Load an image volume from a file
[,SparseBrainVolume,missing,missing,ANY-method
extractor
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.
BrainVolume
BrainBucket
mapToColors
BrainVectorSource
Generic function to convert N-dimensional real world coordinates to grid coordinates
BrainVector
Extract connected components from a 3D mask
Constructor for SurfaceDataMetaInfo
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.
BrainSurfaceSource
NIMLSurfaceFileDescriptor-class
NIMLSurfaceFileDescriptor
BrainFileDescriptor-class
BrainFileDescriptor
as.list,SparseBrainVector-method
as.list
overlay two objects
BrainSource
Generic function to map values from one set to another using a user-supplied lookup table
image
Layer
show an AxisSet1D
MNI SPACE 1MM
BinaryWriter
Kernel
BrainSlice constructor
SurfaceDataMetaInfo-class
SurfaceDataMetaInfo
This class contains meta information for surface-based data (the values that map to a surface geometry)
print a AxisSet3D
instance
as.logical,BrainVolume-method
as.logical
Generic function to test whether a file name conforms to the given BrainFileDescriptor
instance.
Will test for match to header file only
AxisSet2D
given three named axes return AxisSet3D singleton
dim of FileMetaInfo
[[,BrainBucket,index,missing-method
extract labeled volume from BrainBucket
Concatenate two objects
Generic function to extract a sub-vector from a BrainVector
object.
SparseBrainVolume
NamedAxis
[,SparseBrainVector,numeric,missing,ANY-method
extractor
Extract coordinates
as.numeric,SparseBrainVolume-method
Convert SparseBrainVolume to numeric
LogicalBrainVolume
Create a square region of interest where the z-dimension is fixed at one voxel coordinate.
Generic function to extract the number of dimensions of an object
NIfTIFileDescriptor-class
NIfTIFileDescriptor
Create A Cuboid Region of Interest
SparseBrainVector
makeVolume
pick
[,SparseBrainVolume,numeric,missing,missing-method
extractor
Generic function to test whether a file name conforms to the given a BrainFileDescriptor
instance.
Will test for match to data file only
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
Get length of BrainVector
. This is the numbe rof volumes in the volume vector (e.g. the 4th image dimension)
Generic function to get the name of the data file, given a file name and a BrainFileDescriptor
instance.
Constructor for NIfTIMetaInfo
class
Create an exhaustive searchlight iterator
clusterCenters
show an AxisSet3D
DenseBrainVolume
Constructor for SurfaceGeometryMetaInfo
class
show an NamedAxis
imageGrid
[,SparseBrainVolume,matrix,missing,ANY-method
extractor
conversion from DenseBrainVolume to array
Generic function to extract a set of series from a 4D image
sliceData
[,SparseBrainVector,missing,missing,ANY-method
extractor
show,SurfaceGeometryMetaInfo-method
show an SurfaceGeometryMetaInfo
ColumnReader
as.matrix,SparseBrainVector-method
as.matrix
as.raster
dim
NIMLSurfaceDataMetaInfo-class
NIMLSurfaceDataMetaInfo
This class contains meta information for surface-based data for the NIML data format
BrainMetaInfo
This class contains meta information from an image
Generic function to get the name of the header file, given a file name and a BrainFileDescriptor
instance.
extract voxel coordinates
Generic function to convert N-dimensional grid coordinate to 1D indices
Create A Spherical Region of Interest
Generic getter function to extract image axes
Index Lookup operation
print a NamedAxis
Render a slice at z coordinate
print a AxisSet2D
instance
[,SparseBrainVolume,numeric,numeric,ANY-method
extractor
[,ROIVolume,numeric,missing,ANY-method
extract data from ROIVolume
Generic function to apply a function to an object
show a BrainVolume
tesselate
as.vector,BrainData-method
convert BrainData
instance to vector
Base class for image representing 3D volumetric data.
BrainSurface
Generic function to create data reader
read header information of an image file
partition
Convert to a LogicalBrainVolume
Generic function to extract a one or more individual volumes from a four-dimensional image
Convert to from dense to sparse representation
Generic functions to apply a function to each (2D) slice of an image
Generic function to center/scale row-subsets of a matrix or matrix-like object
show an AxisSet2D
neuroim
show,SparseBrainVector-method
show a SparseBrainVector
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.
.isExtension
Generic function to read a sequence of elements from an input source
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
Extract indices
show a BaseMetaInfo
matrixToVolumeList
converts a matrix to a list of BrainVolumes with values filled at grid coordinates determined by the vox
argument.
show a BrainVector
show,BrainVectorSource-method
show a BrainVectorSource
Generic getter to extract image coordinate transformation
numClusters
SurfaceGeometryMetaInfo-class
SurfaceGeometryMetaInfo
This class contains meta information for brain surface geometry
load an surface from a set of files
Generic function to convert 1-dimensional real axis coordinates along a single axis dimension to an 1D index along the same axis
Generic function to convert 1D indices to N-dimensional grid coordinates
Generic function to extract geometric properties of an image.
SparseBrainVectorSource-class
SparseBrainVectorSource
Extract vector series from object
[,BrainBucket,index,missing,ANY-method
extract labeled volume from BrainBucket
show,SurfaceDataMetaInfo-method
show an SurfaceDataMetaInfo
load Freesurfer ascii surface
[,SparseBrainVector,missing,numeric,ANY-method
extractor
show an AxisSet4D
[,SparseBrainVector,numeric,numeric,ANY-method
extractor
Generic function to write a 3D image volume to disk
show an ROIVolime
Extract a 2D slice from an image volume
Render an image to create a drawable image.
Find connected components
Generic function to apply a function to each volume of a four-dimensional image
as.array,BrainData-method
convert BrainData
instance to array
Generic function to read image meta info given a file and a BrainFileDescriptor
instance.
show a BrainSpace
Generic function to strip extension from file name, given a BrainFileDescriptor
instance.
Generic function to write a 4D image vector to disk
given two named axes return AxisSet2D singleton
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.
names,BrainBucketSource-method
names
dim of BrainData
object
as.matrix,BrainData-method
convert BrainData
instance to matrix
loadBucket
Generic function to fill disjoint sets of values with the output of a function
Generic function to extract data values of object
Generic function to write a sequence of elements from an input source
loadVector
makeVector
Generic function to print an object
Generic function to extract the voxel dimensions of an image
Generic getter to extract inverse image coordinate transformation
Extract permutation matrix
show a FileMetaInfo
Generic function to convert 1D indices to N-dimensional real world coordinates
Generic function to read a set of column vector from an input source (e.g. ColumnReader
)
seriesIter
[,SparseBrainVolume,missing,numeric,ANY-method
extractor
Generic function to summarize subsets of an object by first splitting by row and then "reducing" by a summary function