Data Structures for Brain Imaging Data

Documentation for package ‘neuroim2’ version 0.8.1

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A B C D E F G H I K L M N O P Q R S T V W misc

neuroim2: neuroimaging data structures for analysis

-- A --

AbstractSparseNeuroVec-class	AbstractSparseNeuroVec Class
add_dim	Add a Dimension to an Object
add_dim-method	Add a Dimension to an Object
AFNIMetaInfo-class	FileMetaInfo Class
anatomical_axes	Pre-defined anatomical axes
ANT_POST	Pre-defined anatomical axes
Arith-method	Arithmetic Operations for NeuroVec and NeuroVol
Arith-method	Arithmetic Operations for NeuroVol and NeuroVec
Arith-method	This function performs arithmetic operations on two ROIVol objects.
Arith-method	Arithmetic Operations
Arith-methods	Arithmetic Operations
ArrayLike3D-class	ArrayLike3D Class
ArrayLike4D-class	ArrayLike4D Class
ArrayLike5D-class	ArrayLike5D Class
as	conversion from 'NeuroVol' to 'LogicalNeuroVol'
as-ClusteredNeuroVol-DenseNeuroVol	Convert ClusteredNeuroVol to DenseNeuroVol
as.dense	Convert to dense representation
as.dense-method	Coerce ROIVol to DenseNeuroVol using as.dense method
as.list-method	Convert FileBackedNeuroVec to List
as.logical	as.logical
as.logical-method	as.logical
as.mask	Convert to a LogicalNeuroVol
as.mask-method	Convert NeuroVol to a mask
as.matrix	Generic as.matrix Method
as.matrix-method	convert a 'NeuroVec' to a matrix
as.numeric-method	Convert SparseNeuroVol to numeric
as.raster	Generic Method for Converting Objects to Raster Format
as.sparse	Convert to from dense to sparse representation
as.sparse-method	Convert DenseNeuroVec to sparse representation using mask
as_nifti_header	Construct a Minimal NIfTI-1 Header from a NeuroVol
axes	Extract Image Axes
axes-method	Extract Image Axes
AxisSet-class	AxisSet
AxisSet1D-class	AxisSet1D
AxisSet2D-class	AxisSet2D
AxisSet3D-class	AxisSet3D Class
AxisSet4D-class	AxisSet4D Class
AxisSet5D-class	AxisSet5D Class

-- B --

BigNeuroVec	Create a Memory-Mapped Neuroimaging Vector
BigNeuroVec-class	BigNeuroVec Class
bilateral_filter	Apply a bilateral filter to a volumetric image
BinaryReader	Create Binary Reader Object
BinaryReader-class	BinaryReader Class
BinaryWriter	Create Binary Writer Object
BinaryWriter-class	BinaryWriter Class
bootstrap_searchlight	Create a bootstrap spherical searchlight iterator
bounds	Extract Spatial Bounds of an Image
bounds-method	Extract Spatial Bounds of an Image

-- C --

centroid	return the centroid of an object
centroid-method	return the centroid of an object
centroids	Return a matrix of centroids of an object
centroids-method	Return a matrix of centroids of an object
close-method	Close a BinaryReader or BinaryWriter
ClusteredNeuroVol	ClusteredNeuroVol Class
ClusteredNeuroVol-class	ClusteredNeuroVol Class
clustered_searchlight	Create a clustered searchlight iterator
coerce-method	Convert ClusteredNeuroVol to DenseNeuroVol
ColumnReader	Create Column Reader Object
ColumnReader-class	ColumnReader
Compare-method	Comparison Operations
Compare-methods	Comparison Operations
concat	Concatenate two objects in the time dimension
concat-method	Concatenate two objects in the time dimension
conn_comp	Connected components
conn_comp-method	Connected components
conn_comp_3D	Extract Connected Components from a 3D Binary Mask
coords	Extract coordinates from an object
coords-method	Extract Coordinates from an IndexLookupVol Object
coord_to_grid	convert n-dimensional real world coordinates to grid coordinates
coord_to_grid-method	convert n-dimensional real world coordinates to grid coordinates
coord_to_index	convert n-dimensional real world coordinates to 1D indices
coord_to_index-method	convert n-dimensional real world coordinates to 1D indices
createNIfTIHeader	Create an Empty NIfTI-1 Header List
cuboid_roi	Create A Cuboid Region of Interest

-- D --

data_file	Generic function to get the name of the data file, given a file name and a 'FileFormat' instance.
data_file-method	Generic function to get the name of the data file, given a file name and a 'FileFormat' instance.
data_file_matches	Generic function to test whether a file name conforms to the given a 'FileFormat' instance. Will test for match to data file only
data_file_matches-method	Generic function to test whether a file name conforms to the given a 'FileFormat' instance. Will test for match to data file only
data_reader	Create a Data Reader
data_reader-method	Create Data Reader for AFNI Format
DenseNeuroVec	DenseNeuroVec Class
DenseNeuroVec-class	DenseNeuroVec Class
DenseNeuroVol	DenseNeuroVol Class
DenseNeuroVol-class	DenseNeuroVol Class
dim	Get Dimensions of FileMetaInfo Object
dim-method	Get Dimensions of FileMetaInfo Object
dim_of	Get the length of a given dimension of an object
dim_of-method	Get the length of a given dimension of an object
drop	Generic Drop Method
drop-method	Drop a dimension
drop_dim	Drop a Dimension from an Object
drop_dim-method	Drop a Dimension from an Object

-- E --

embed_kernel	Generic function to position kernel in a position in image space
embed_kernel-method	Generic function to position kernel in a position in image space
extractor3d	Array-like access for 3-dimensional data structures
extractor4d	Array-like access for 4-dimensional data structures

-- F --

FileBackedNeuroVec	Create a File-Backed Neuroimaging Vector
FileBackedNeuroVec-class	FileBackedNeuroVec Class
FileFormat-class	FileFormat Class
FileFormat-operations	File Format Operations for Neuroimaging Data
FileMetaInfo-class	FileMetaInfo Class
FileSource-class	FileSource Class
file_matches	Generic function to test whether a file name conforms to the given 'FileFormat' instance. Will test for match to either header file or data file
file_matches-method	Generic function to test whether a file name conforms to the given 'FileFormat' instance. Will test for match to either header file or data file
findAnatomy3D	Find 3D anatomical orientation from axis abbreviations

-- G --

gaussian_blur	Gaussian Blur for Volumetric Images
grid_to_coord	Generic function to convert N-dimensional grid coordinates to real world coordinates
grid_to_coord-method	Generic function to convert N-dimensional grid coordinates to real world coordinates
grid_to_grid	Generic function to convert voxel coordinates in the reference space (LPI) to native array space.
grid_to_grid-method	Generic function to convert voxel coordinates in the reference space (LPI) to native array space.
grid_to_index	Generic function to convert N-dimensional grid coordinates to 1D indices
grid_to_index-method	Generic function to convert N-dimensional grid coordinates to 1D indices
guided_filter	Edge-Preserving Guided Filter for Volumetric Images

-- H --

header_file	Generic function to get the name of the header file, given a file name and a 'FileFormat' instance.
header_file-method	Generic function to get the name of the header file, given a file name and a 'FileFormat' instance.
header_file_matches	Generic function to test whether a file name conforms to the given 'FileFormat' instance. Will test for match to header file only
header_file_matches-method	Generic function to test whether a file name conforms to the given 'FileFormat' instance. Will test for match to header file only

-- I --

image	Generic Image Method for Creating Visual Representations
IndexLookupVol	IndexLookupVol Class
IndexLookupVol-class	IndexLookupVol Class
index_to_coord	convert 1d indices to n-dimensional real world coordinates
index_to_coord-method	convert 1d indices to n-dimensional real world coordinates
index_to_grid	Convert 1d indices to n-dimensional grid coordinates
index_to_grid-method	Convert 1d indices to n-dimensional grid coordinates
indices	Extract indices
indices-method	Get Indices from an IndexLookupVol Object
INF_SUP	Pre-defined anatomical axes
inverse_trans	Extract inverse image coordinate transformation
inverse_trans-method	Extract inverse image coordinate transformation

-- K --

Kernel	Create a Kernel object from a function of distance from kernel center
Kernel-class	Kernel

-- L --

laplace_enhance	Laplacian Enhancement Filter for Volumetric Images
LEFT_RIGHT	Pre-defined anatomical axes
length-method	Get length of NeuroVec object
linear_access	Extract values from an array-like object using linear indexing.
linear_access-method	Linear Access Method for FileBackedNeuroVec
load_data-method	Load image data from a NeuroVecSource object
LogicalNeuroVol	LogicalNeuroVol Class
LogicalNeuroVol-class	LogicalNeuroVol Class
lookup	Index Lookup operation
lookup-method	Lookup Values in an IndexLookupVol Object

-- M --

mapf	Apply a function to an object.
mapf-method	Apply a function to an object.
MappedNeuroVec	MappedNeuroVec Class
MappedNeuroVec-class	MappedNeuroVec Class
MappedNeuroVecSource	MappedNeuroVecSource Class
MappedNeuroVecSource-class	MappedNeuroVecSource Class
map_values	Map Values from One Set to Another Using a User-supplied Lookup Table
map_values-method	Map Values from One Set to Another Using a User-supplied Lookup Table
matricized_access	Extract values from a 4D tensor using a matrix of time-space indices.
matricized_access-method	Extract values from a 4D tensor using a matrix of time-space indices.
matrixToQuatern	Convert a Transformation Matrix to a Quaternion Representation
MetaInfo	Create Neuroimaging Metadata Object
MetaInfo-class	MetaInfo Class

-- N --

NamedAxis-class	NamedAxis
ndim	Extract the number of dimensions of an object
ndim-method	Get number of dimensions in axis set
ndim-method	Extract the number of dimensions of an object
neuro-ops	Arithmetic and Comparison Operations for Neuroimaging Objects
neuro-resample	Resampling Methods for Neuroimaging Objects
NeuroBucket-class	NeuroBucket
NeuroHyperVec	Constructor for NeuroHyperVec class
NeuroHyperVec-class	NeuroHyperVec Class
neuroim2	neuroim2: neuroimaging data structures for analysis
NeuroObj-class	NeuroObj Class
NeuroSlice	NeuroSlice: 2D Neuroimaging Data Container
NeuroSlice-class	NeuroSlice Class
NeuroSpace	NeuroSpace: Spatial Reference System for Neuroimaging Data
NeuroSpace-class	NeuroSpace Class
NeuroVec	NeuroVec Class
NeuroVec-class	NeuroVec Class
NeuroVecSeq	NeuroVecSeq: A Container for Sequential NeuroVec Objects
NeuroVecSeq-class	NeuroVecSeq Class
NeuroVecSource	NeuroVecSource
NeuroVecSource-class	NeuroVecSource Class
NeuroVol	NeuroVol: 3D Neuroimaging Volume Class
NeuroVol-class	NeuroVol Class
NeuroVolSource	Constructor for NeuroVolSource
NIFTIMetaInfo	Create NIFTI Format Metadata Object
NIFTIMetaInfo-class	FileMetaInfo Class
None	Pre-defined null axis
NullAxis	Pre-defined null axis set
numericOrMatrix-class	numericOrMatrix Union
num_clusters	Number of Clusters
num_clusters-method	Number of Clusters

-- O --

OrientationList2D	Pre-defined 2D orientation configurations
OrientationList3D	Pre-defined 3D orientation configurations
origin	Extract Image Origin
origin-method	Extract Image Origin

-- P --

partition	Partition an image into a set of disjoint clusters
partition-method	Partition an image into a set of disjoint clusters
patch_set	Generate a set of coordinate "patches" of fixed size from an image object.
patch_set-method	Create a patch set from a NeuroVol object
perm_mat	Extract permutation matrix associated with an image
perm_mat-method	Get permutation matrix from axis set
perm_mat-method	Get permutation matrix from axis set
perm_mat-method	Extract permutation matrix associated with an image
plot-method	Plot a NeuroSlice
POST_ANT	Pre-defined anatomical axes

-- Q --

quaternToMatrix

Convert Quaternion Parameters to a Transformation Matrix

-- R --

random_searchlight	Create a spherical random searchlight iterator
read_elements-method	Read Elements from Binary Reader
read_header	read header information of an image file
read_meta_info	Generic function to read image meta info given a file
read_meta_info-method	Generic function to read image meta info given a file
read_vec	read_vec
read_vol	Load an image volume from a file
read_vol_list	read_vol_list
reorient	Remap the grid-to-world coordinates mapping of an image.
reorient-method	Remap the grid-to-world coordinates mapping of an image.
resample	Resample an Image to Match the Space of Another Image
resample-method	Resample an Image to Match the Space of Another Image
RIGHT_LEFT	Pre-defined anatomical axes
ROI-class	ROI
ROICoords	Create ROI Coordinates Object
ROICoords-class	ROICoords
ROIVec	Create an instance of class 'ROIVec'
ROIVec-class	ROIVec
ROIVecWindow-class	ROIVecWindow
ROIVol	Create ROI Volume Object
ROIVol-class	ROIVol
ROIVolWindow-class	ROIVolWindow

-- S --

scale	Generic Scale Method
scale_series	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.
scale_series-method	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.
searchlight	Create an exhaustive searchlight iterator
searchlight-methods	Searchlight Analysis Methods
searchlight_coords	Create an exhaustive searchlight iterator for voxel coordinates using spherical_roi
series	Extract one or more series from object
series-method	Series method for NeuroHyperVec
series-method	Extract one or more series from object
series_roi	Extract time series from specific voxel coordinates and return as ROI object
series_roi-method	Extract one or more series from object
show-method	Show method for NamedAxis objects
slice	Extract image slice
slice-method	Extract image slice
slices	Extract an ordered series of 2D slices from a 3D or 4D object
slices-method	Extract an ordered series of 2D slices from a 3D or 4D object
space	Extract Geometric Properties of an Image
space-method	Extract Geometric Properties of an Image
spacing	Extract Voxel Dimensions of an Image
spacing-method	Extract Voxel Dimensions of an Image
SparseNeuroVec	SparseNeuroVec Class
SparseNeuroVec-class	SparseNeuroVec Class
SparseNeuroVecSource-class	SparseNeuroVecSource Class
SparseNeuroVol	SparseNeuroVol Class
SparseNeuroVol-class	SparseNeuroVol Class
spatial-filter	Spatial Filtering Methods for Neuroimaging Data
spherical_roi	Create a Spherical Region of Interest
spherical_roi_set	Create Multiple Spherical Regions of Interest
split_blocks	Cut a vector-valued object into a list of sub-blocks
split_blocks-method	Cut a vector-valued object into a list of sub-blocks
split_clusters	Cut an object into a list of spatial or spatiotemporal clusters
split_clusters-method	Cut an object into a list of spatial or spatiotemporal clusters
split_fill	Fill Disjoint Sets of Values with the Output of a Function
split_fill-method	Fill Disjoint Sets of Values with the Output of a Function
split_reduce	Summarize Subsets of an Object by Splitting by Row and Applying a Summary Function
split_reduce-method	Summarize Subsets of an Object by Splitting by Row and Applying a Summary Function
split_scale	Center and/or Scale Row-subsets of a Matrix or Matrix-like Object
split_scale-method	Center and/or Scale Row-subsets of a Matrix or Matrix-like Object
square_roi	Create a square region of interest
strip_extension	Generic function to strip extension from file name, given a 'FileFormat' instance.
strip_extension-method	Generic function to strip extension from file name, given a 'FileFormat' instance.
sub_vector	Generic function to extract a sub-vector from a 'NeuroVec' object.
sub_vector-method	Generic function to extract a sub-vector from a 'NeuroVec' object.
Summary-method	Summary method for Neuroimaging objects
SUP_INF	Pre-defined anatomical axes

-- T --

TIME	Time axis
TimeAxis	Time axis set
trans	Extract image coordinate transformation
trans-method	Extract image coordinate transformation

-- V --

values	Extract Data Values of an Object
values-method	Extract Data Values of an Object
vectors	Extract an ordered list of 1D vectors.
vectors-method	Extract an ordered list of 1D vectors.
vols	Extract an ordered series of 3D volumes.
vols-method	Extract an ordered series of 3D volumes.
voxels	extract voxel coordinates
voxels-method	extract voxel coordinates

-- W --

which_dim	Find Dimensions of a Given Axis
which_dim-method	Find Dimensions of a Given Axis
write_elements	Write a sequence of elements from an input source
write_elements-method	Write a sequence of elements from an input source
write_vec	Write a 4d image vector to disk
write_vec-method	Write a 4d image vector to disk
write_vol	Write a 3d image volume to disk
write_vol-method	Write a 3d image volume to disk

-- misc --

[	Extract or replace parts of an object
[-method	NeuroHyperVec Class
[-method	Extract or replace parts of an object
[-method	Array-like access for 3-dimensional data structures
[-method	Array-like access for 4-dimensional data structures
[-method	Extractor Method for AbstractSparseNeuroVec
[.NeuroHyperVec	NeuroHyperVec Class
[[-method	Extract Element from NeuroVecSeq
[[-method	[[
[[-method	[[