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Constructors

Constructors for creating and initializing various neuroimaging objects

AbstractSparseNeuroVec-class
AbstractSparseNeuroVec Class
AFNIMetaInfo()
Create AFNI Format Metadata Object
ArrayLike3D-class
ArrayLike3D Class
ArrayLike4D-class
ArrayLike4D Class
ArrayLike5D-class
ArrayLike5D Class
AxisSet-class
AxisSet
AxisSet1D-class
AxisSet1D
AxisSet2D-class
AxisSet2D
AxisSet3D-class
AxisSet3D Class
AxisSet4D-class
AxisSet4D Class
AxisSet5D-class
AxisSet5D Class
BigNeuroVec-class
BigNeuroVec Class
BigNeuroVec()
Create a Memory-Mapped Neuroimaging Vector
BinaryReader()
Create Binary Reader Object
BinaryWriter()
Create Binary Writer Object
BinaryWriter-class
BinaryWriter Class
ClusteredNeuroVol()
ClusteredNeuroVol Class
DenseNeuroVec()
DenseNeuroVec Class
DenseNeuroVol()
DenseNeuroVol Class
FileBackedNeuroVec()
Create a File-Backed Neuroimaging Vector
IndexLookupVol()
IndexLookupVol Class
LogicalNeuroVol()
LogicalNeuroVol Class
MappedNeuroVec()
MappedNeuroVec Class
MetaInfo-class
MetaInfo Class
MetaInfo()
Create Neuroimaging Metadata Object
NeuroBucket-class
NeuroBucket
`[`(<NeuroHyperVec>,<ANY>,<ANY>,<ANY>)
NeuroHyperVec Class
NeuroHyperVec()
Constructor for NeuroHyperVec class
NeuroObj-class
NeuroObj Class
NeuroSlice()
NeuroSlice: 2D Neuroimaging Data Container
NeuroSpace()
NeuroSpace: Spatial Reference System for Neuroimaging Data
NeuroVec()
NeuroVec Class
NeuroVecSeq()
NeuroVecSeq: A Container for Sequential NeuroVec Objects
NeuroVecSource()
NeuroVecSource
NeuroVecSource-class
NeuroVecSource Class
NeuroVolSource()
Constructor for NeuroVolSource
NeuroVol()
NeuroVol: 3D Neuroimaging Volume Class
NIFTIMetaInfo()
Create NIFTI Format Metadata Object
ROICoords-class
ROICoords
ROICoords()
Create ROI Coordinates Object
ROIVec()
Create an instance of class ROIVec
ROIVol()
Create ROI Volume Object
SparseNeuroVec()
SparseNeuroVec Class
SparseNeuroVol()
SparseNeuroVol Class
TimeAxis
Time axis set
NullAxis
Pre-defined null axis set
numericOrMatrix-class
numericOrMatrix Union

S4 Classes

S4 classes for various neuroimaging objects

BinaryReader-class
BinaryReader Class
ColumnReader-class
ColumnReader
FileBackedNeuroVec-class
FileBackedNeuroVec Class
FileFormat-class
FileFormat Class
FileFormat-operations
File Format Operations for Neuroimaging Data
FileMetaInfo-class NIFTIMetaInfo-class AFNIMetaInfo-class
FileMetaInfo Class
FileSource-class
FileSource Class
MappedNeuroVecSource()
MappedNeuroVecSource Class
NamedAxis-class
NamedAxis
NeuroSlice-class
NeuroSlice Class
NeuroSpace-class
NeuroSpace Class
NeuroVecSeq-class
NeuroVecSeq Class
NeuroVol-class
NeuroVol Class
ROI-class
ROI
ROIVec-class
ROIVec
ROIVecWindow-class
ROIVecWindow
ROIVol-class
ROIVol
ROIVolWindow-class
ROIVolWindow
SparseNeuroVecSource-class
SparseNeuroVecSource Class
OrientationList2D
Pre-defined 2D orientation configurations
OrientationList3D
Pre-defined 3D orientation configurations

Data Loading and Manipulation

Methods for loading and manipulating neuroimaging data

concat()
Concatenate two objects in the time dimension
mapf()
Apply a function to an object.
vols()
Extract an ordered series of 3D volumes.
neuroim2-package neuroim2
neuroim2: neuroimaging data structures for analysis
data_file()
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_reader()
Create a Data Reader
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
read_elements()
Read a sequence of elements from an input source
createNIfTIHeader()
Create an Empty NIfTI-1 Header List
linear_access()
Extract values from an array-like object using linear indexing.
image
Generic Image Method for Creating Visual Representations
scale()
Generic Scale Method

Coordinate and Dimension Operations

Methods for operating on coordinates and dimensions

space()
Extract Geometric Properties of an Image
axes()
Extract Image Axes
spacing()
Extract Voxel Dimensions of an Image
bounds()
Extract Spatial Bounds of an Image
centroid()
return the centroid of an object
coord_to_grid()
convert n-dimensional real world coordinates to grid coordinates
coord_to_index()
convert n-dimensional real world coordinates to 1D indices
grid_to_coord()
Generic function to convert N-dimensional grid coordinate coordinates to real world coordinates
grid_to_index()
Generic function to convert N-dimensional grid coordinate to 1D indices
grid_to_grid()
Generic function to convert voxel coordinates in the reference space (LPI) to native array space.
index_to_coord()
convert 1d indices to n-dimensional real world coordinates
index_to_grid()
Convert 1d indices to n-dimensional grid coordinates
dim_of()
Get the length of a given dimension of an object
drop_dim()
Drop a Dimension from an Object
add_dim()
Add a Dimension to an Object
ndim()
Extract the number of dimensions of an object
voxels()
extract voxel coordinates
which_dim()
Find Dimensions of a Given Axis
trans()
Extract image coordinate transformation
inverse_trans()
Extract inverse image coordinate transformation
origin()
Extract Image Origin
perm_mat()
Extract permutation matrix associated with an image
strip_extension()
Generic function to strip extension from file name, given a FileFormat instance.
LEFT_RIGHT RIGHT_LEFT ANT_POST POST_ANT INF_SUP SUP_INF
Pre-defined anatomical axes
TIME
Time axis
findAnatomy3D()
Find 3D anatomical orientation from axis abbreviations
matrixToQuatern()
Convert a Transformation Matrix to a Quaternion Representation
quaternToMatrix()
Convert Quaternion Parameters to a Transformation Matrix

ROI and Clustering

Methods for working with regions of interest and clustering

partition()
Partition an image into a set of disjoint clusters
patch_set()
Generate a set of coordinate "patches" of fixed size from an image object.
split_clusters()
Cut an object into a list of spatial or spatiotemporal clusters
centroids()
Return a matrix of centroids of an object
conn_comp()
Connected components
conn_comp_3D()
Extract Connected Components from a 3D Binary Mask
coords()
Extract coordinates from an object
cuboid_roi()
Create A Cuboid Region of Interest
num_clusters()
Number of Clusters
slices()
Extract an ordered series of 2D slices from a 3D or 4D object
slice()
Extract image slice
vectors()
Extract an ordered list of 1D vectors.
values()
Extract Data Values of an Object
spherical_roi_set()
Create Multiple Spherical Regions of Interest

Kernel and Extraction

Methods for kernel operations and feature extraction

Kernel()
Create a Kernel object from a function of distance from kernel center
Kernel-class
Kernel
embed_kernel()
Generic function to position kernel in a postion in image space
`[`(<ArrayLike3D>,<numeric>,<missing>,<ANY>) `[`(<ArrayLike3D>,<matrix>,<missing>,<ANY>) `[`(<ArrayLike3D>,<missing>,<missing>,<ANY>) `[`(<ArrayLike3D>,<missing>,<numeric>,<ANY>)
Array-like access for 3-dimensional data structures
`[`(<ArrayLike4D>,<matrix>,<missing>,<ANY>) `[`(<ArrayLike4D>,<numeric>,<numeric>,<ANY>) `[`(<ArrayLike4D>,<numeric>,<missing>,<ANY>) `[`(<ArrayLike4D>,<integer>,<missing>,<ANY>) `[`(<ArrayLike4D>,<missing>,<missing>,<ANY>) `[`(<ArrayLike4D>,<missing>,<numeric>,<ANY>)
Array-like access for 4-dimensional data structures
spherical_roi()
Create a Spherical Region of Interest
square_roi()
Create a square region of interest
searchlight()
Create an exhaustive searchlight iterator
searchlight_coords()
Create an exhaustive searchlight iterator for voxel coordinates using spherical_roi
random_searchlight()
Create a spherical random searchlight iterator
bootstrap_searchlight()
Create a bootstrap spherical searchlight iterator
series_roi()
Extract time series from specific voxel coordinates and return as ROI object
gaussian_blur()
Gaussian Blur for Volumetric Images
guided_filter()
Edge-Preserving Guided Filter for Volumetric Images
bilateral_filter()
Apply a bilateral filter to a volumetric image
reorient()
Remap the grid-to-world coordinates mapping of an image.
clustered_searchlight()
Create a clustered searchlight iterator
spatial-filter
Spatial Filtering Methods for Neuroimaging Data
searchlight-methods
Searchlight Analysis Methods
laplace_enhance()
Laplacian Enhancement Filter for Volumetric Images

Lookup and Mapping

Methods for looking up and mapping neuroimaging data

lookup()
Index Lookup operation
map_values()
Map Values from One Set to Another Using a User-supplied Lookup Table
resample()
Resample an Image to Match the Space of Another Image
neuro-resample
Resampling Methods for Neuroimaging Objects

Data Access and Indexing

Methods for accessing and indexing neuroimaging data

sub_vector()
Generic function to extract a sub-vector from a NeuroVec object.
indices()
Extract indices
length(<NeuroVec>) length(<NeuroVecSeq>) length(<ROIVol>) length(<ROICoords>)
Get length of NeuroVec object
neuro-ops
Arithmetic and Comparison Operations for Neuroimaging Objects

Scaling and Resampling

Methods for splitting, scaling, processing, and resampling neuroimaging data

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.
resample()
Resample an Image to Match the Space of Another Image
split_blocks()
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_fill()
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_scale()
Center and/or Scale Row-subsets of a Matrix or Matrix-like Object

Visualization and Rendering

Methods for visualizing and rendering neuroimaging data

render()
Render an image to create a drawable image.
render_slice()
Render a slice at z coordinate

IO

Methods for input-output operations

read_vec()
read_vec
read_vol()
Load an image volume from a file
write_elements()
Write a sequence of elements from an input source
write_vec()
Write a 4d image vector to disk
write_vol()
Write a 3d image volume to disk
close(<BinaryReader>) close(<BinaryWriter>)
Close a BinaryReader or BinaryWriter
ColumnReader()
Create Column Reader Object
header_file()
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
read_columns()
Read a set of column vector from an input source (e.g. ColumnReader)
read_header()
read header information of an image file
read_meta_info()
Generic function to read image meta info given a file
read_vol_list()
read_vol_list

Miscellaneous

Miscellaneous methods and functions

`[`(<NeuroHyperVec>,<ANY>,<ANY>,<ANY>)
NeuroHyperVec Class
`[[`(<NeuroVecSeq>,<numeric>)
Extract Element from NeuroVecSeq
`[[`(<SparseNeuroVec>,<numeric>)
[[
`[`(<ROIVol>,<numeric>,<missing>,<ANY>) `[`(<ROIVol>,<logical>,<missing>,<ANY>)
Extract or replace parts of an object
`[`(<ArrayLike3D>,<numeric>,<missing>,<ANY>) `[`(<ArrayLike3D>,<matrix>,<missing>,<ANY>) `[`(<ArrayLike3D>,<missing>,<missing>,<ANY>) `[`(<ArrayLike3D>,<missing>,<numeric>,<ANY>)
Array-like access for 3-dimensional data structures
`[`(<ArrayLike4D>,<matrix>,<missing>,<ANY>) `[`(<ArrayLike4D>,<numeric>,<numeric>,<ANY>) `[`(<ArrayLike4D>,<numeric>,<missing>,<ANY>) `[`(<ArrayLike4D>,<integer>,<missing>,<ANY>) `[`(<ArrayLike4D>,<missing>,<missing>,<ANY>) `[`(<ArrayLike4D>,<missing>,<numeric>,<ANY>)
Array-like access for 4-dimensional data structures
`[`(<AbstractSparseNeuroVec>,<numeric>,<numeric>,<ANY>)
Extractor Method for AbstractSparseNeuroVec
`[[`(<NeuroVec>,<numeric>)
[[
dim(<NeuroSpace>)
dim
dim(<FileMetaInfo>) dim(<NeuroObj>) dim(<ROIVol>) dim(<ROICoords>)
Get Dimensions of FileMetaInfo Object
dim_of()
Get the length of a given dimension of an object
drop(<NeuroVec>)
drop
drop()
Generic Drop Method
drop_dim(<AxisSet2D>,<missing>)
Drop dimension from axis set
drop_dim(<AxisSet2D>,<numeric>)
Drop dimension from axis set
drop_dim(<AxisSet3D>,<missing>)
Drop dimension from axis set
drop_dim(<AxisSet3D>,<numeric>)
Drop dimension from axis set
drop_dim()
Drop a Dimension from an Object
length(<NeuroVec>) length(<NeuroVecSeq>) length(<ROIVol>) length(<ROICoords>)
Get length of NeuroVec object
show(<AxisSet1D>)
Show method for AxisSet1D objects
show(<AxisSet2D>)
Show method for AxisSet2D objects
show(<AxisSet3D>)
Show method for AxisSet3D objects
show(<AxisSet4D>)
Show method for AxisSet4D objects
show(<ClusteredNeuroVol>)
Display ClusteredNeuroVol Information
show(<FileMetaInfo>)
show a FileMetaInfo
show(<MappedNeuroVec>)
Show Method for MappedNeuroVec Objects
show(<NamedAxis>)
Show method for NamedAxis objects
show(<NeuroHyperVec>)
Show NeuroHyperVec Object
show(<NeuroVec>)
show a NeuroVec object
show(<NeuroVecSource>)
show a NeuroVecSource object
show(<NeuroVol>)
Display NeuroVol Object
show(<ROIVec>)
show an ROIVec
show(<ROIVol>)
show an ROIVol
show(<SparseNeuroVec>)
show a SparseNeuroVec
show(<SparseNeuroVol>)
show a SparseNeuroVol
show(<IndexLookupVol>) show(<NeuroSlice>) show(<NeuroSpace>) show(<DenseNeuroVec>) show(<NeuroVecSeq>) show(<ROICoords>)
Show method for IndexLookupVol Objects
as-ClusteredNeuroVol-DenseNeuroVol coerce,ClusteredNeuroVol,DenseNeuroVol-method
Convert ClusteredNeuroVol to DenseNeuroVol
as
conversion from NeuroVol to LogicalNeuroVol
as.dense(<ClusteredNeuroVol>) as.dense(<ROIVol>)
Coerce ROIVol to DenseNeuroVol using as.dense method
as.dense()
Convert to dense representation
as.list(<FileBackedNeuroVec>) as.list(<NeuroVec>) as.list(<SparseNeuroVec>)
Convert FileBackedNeuroVec to List
as.logical(<NeuroVol>) as.logical(<ROIVol>)
as.logical
as.mask(<NeuroVol>,<missing>) as.mask(<NeuroVol>,<numeric>)
Convert NeuroVol to a mask
as.mask()
Convert to a LogicalNeuroVol
as.matrix(<MappedNeuroVec>) as.matrix(<NeuroVec>) as.matrix(<DenseNeuroVec>) as.matrix(<ROIVec>) as.matrix(<SparseNeuroVec>)
convert a NeuroVec to a matrix
as.matrix()
Generic as.matrix Method
as.numeric(<SparseNeuroVol>) as.numeric(<ROIVol>)
Convert SparseNeuroVol to numeric
as.raster
Generic Method for Converting Objects to Raster Format
as.sparse(<DenseNeuroVec>,<LogicalNeuroVol>) as.sparse(<DenseNeuroVec>,<numeric>) as.sparse(<DenseNeuroVol>,<LogicalNeuroVol>) as.sparse(<DenseNeuroVol>,<numeric>) as.sparse(<ROIVol>,<ANY>)
Convert DenseNeuroVec to sparse representation using mask
as.sparse()
Convert to from dense to sparse representation
as_nifti_header()
Construct a Minimal NIfTI-1 Header from a NeuroVol
close(<BinaryReader>) close(<BinaryWriter>)
Close a BinaryReader or BinaryWriter
plot(<NeuroSlice>) plot(<NeuroVol>)
Plot a NeuroSlice
Arith(<NeuroVec>,<NeuroVol>)
Arithmetic Operations for NeuroVec and NeuroVol
Arith(<NeuroVol>,<NeuroVec>)
Arithmetic Operations for NeuroVol and NeuroVec
Arith(<ROIVol>,<ROIVol>)
This function performs arithmetic operations on two ROIVol objects.
Arith(<SparseNeuroVol>,<SparseNeuroVol>) Arith(<DenseNeuroVol>,<DenseNeuroVol>) Arith(<DenseNeuroVec>,<DenseNeuroVec>) Arith(<SparseNeuroVol>,<NeuroVol>) Arith(<NeuroVol>,<SparseNeuroVol>) Arith(<NeuroVec>,<NeuroVec>) Arith(<SparseNeuroVec>,<SparseNeuroVec>)
Arithmetic Operations
Compare(<SparseNeuroVol>,<numeric>) Compare(<numeric>,<SparseNeuroVol>) Compare(<NeuroVec>,<NeuroVec>)
Comparison Operations
Summary(<SparseNeuroVec>) Summary(<SparseNeuroVol>) Summary(<DenseNeuroVol>)
Summary method for Neuroimaging objects
add_dim()
Add a Dimension to an Object
axes()
Extract Image Axes
bounds()
Extract Spatial Bounds of an Image
centroid()
return the centroid of an object
centroids()
Return a matrix of centroids of an object
concat()
Concatenate two objects in the time dimension
conn_comp()
Connected components
coord_to_grid()
convert n-dimensional real world coordinates to grid coordinates
coord_to_index()
convert n-dimensional real world coordinates to 1D indices
coords(<IndexLookupVol>) coords(<ROIVol>) coords(<ROICoords>) coords(<AbstractSparseNeuroVec>)
Extract Coordinates from an IndexLookupVol Object
data_file()
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_reader(<NIFTIMetaInfo>) data_reader(<AFNIMetaInfo>)
Create Data Reader for AFNI Format
embed_kernel()
Generic function to position kernel in a postion in image space
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
grid_to_coord()
Generic function to convert N-dimensional grid coordinate 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_index()
Generic function to convert N-dimensional grid coordinate to 1D indices
header_file()
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
index_to_coord()
convert 1d indices to n-dimensional real world coordinates
index_to_grid()
Convert 1d indices to n-dimensional grid coordinates
inverse_trans()
Extract inverse image coordinate transformation
linear_access(<FileBackedNeuroVec>,<numeric>) linear_access(<MappedNeuroVec>,<numeric>) linear_access(<NeuroHyperVec>,<ANY>) linear_access(<NeuroVecSeq>,<numeric>) linear_access(<SparseNeuroVol>,<numeric>) linear_access(<AbstractSparseNeuroVec>,<numeric>)
Linear Access Method for FileBackedNeuroVec
load_data(<MappedNeuroVecSource>) load_data(<NeuroVecSource>) load_data(<NeuroVolSource>) load_data(<SparseNeuroVecSource>)
Load image data from a NeuroVecSource object
mapf()
Apply a function to an object.
map_values()
Map Values from One Set to Another Using a User-supplied Lookup Table
matricized_access()
Extract values from a matricized (x,y,z) of a 4D tensor using a space-time coordinate matrix.
ndim(<AxisSet>)
Get number of dimensions in axis set
ndim()
Extract the number of dimensions of an object
num_clusters(<ClusteredNeuroVol>)
Number of Clusters
origin()
Extract Image Origin
partition()
Partition an image into a set of disjoint clusters
patch_set(<NeuroVol>,<numeric>,<missing>) patch_set(<NeuroVol>,<numeric>,<LogicalNeuroVol>)
Create a patch set from a NeuroVol object
perm_mat(<AxisSet2D>)
Get permutation matrix from axis set
perm_mat(<AxisSet3D>)
Get permutation matrix from axis set
perm_mat(<NeuroSpace>)
Get permutation matrix from axis set
read_columns()
Read a set of column vector from an input source (e.g. ColumnReader)
read_elements(<BinaryReader>,<numeric>)
Read Elements from Binary Reader
read_meta_info()
Generic function to read image meta info given a file
reorient()
Remap the grid-to-world coordinates mapping of an image.
resample()
Resample an Image to Match the Space of Another Image
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.
series(<NeuroHyperVec>,<ANY>)
Series method for NeuroHyperVec
series() series_roi(<NeuroVec>,<matrix>) series_roi(<NeuroVec>,<ROICoords>) series_roi(<NeuroVec>,<LogicalNeuroVol>) series_roi(<NeuroVec>,<numeric>) series_roi(<NeuroVecSeq>,<matrix>)
Extract one or more series from object
slice()
Extract image slice
slices()
Extract an ordered series of 2D slices from a 3D or 4D object
space()
Extract Geometric Properties of an Image
spacing()
Extract Voxel Dimensions of an Image
split_blocks()
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_fill()
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_scale()
Center and/or Scale Row-subsets of a Matrix or Matrix-like Object
strip_extension()
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.
trans()
Extract image coordinate transformation
values()
Extract Data Values of an Object
vectors()
Extract an ordered list of 1D vectors.
vols()
Extract an ordered series of 3D volumes.
voxels()
extract voxel coordinates
which_dim()
Find Dimensions of a Given Axis
write_elements(<BinaryWriter>,<numeric>)
Write Elements to Binary Writer
write_vec()
Write a 4d image vector to disk
write_vol()
Write a 3d image volume to disk
None
Pre-defined null axis