# Data Structures for Brain Imaging Data

## Documentation for package ‘neuroim2’ version 0.8.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

neuroim2-package | 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
annotate_orientation | Add L/R and A/P/S/I annotations (optional)
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.array | Generic as.array Method
as.array-method | Convert ClusteredNeuroVol to a base array
as.array-method | Convert SparseNeuroVol to a base array
as.dense | Convert to dense representation
as.dense-method | Coerce SparseNeuroVol to DenseNeuroVol
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.vector-method | Convert SparseNeuroVol to a base vector
as_mmap | Convert a NeuroVec to a memory-mapped representation
as_mmap-method | Convert a NeuroVec to a memory-mapped representation
as_mmap-methods | Convert a NeuroVec to a memory-mapped representation
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
bilateral_filter_4d | Apply a 4D bilateral filter to a NeuroVec
BinaryReader | Create Binary Reader Object
BinaryReader-class | BinaryReader Class
BinaryWriter | Create Binary Writer Object
BinaryWriter-class | BinaryWriter Class
blobby_shape | Convenience shape generators for 'resampled_searchlight()'
bootstrap_searchlight | Create a resampled 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
cgb_filter | Correlation-guided bilateral filtering (convenience wrapper)
cgb_make_graph | Build a correlation-guided bilateral (CGB) graph
cgb_smooth | Apply a precomputed CGB graph to volumetric data
cgb_smooth_loro | Leave-one-run-out smoothing helper
close-method | Close a BinaryReader or BinaryWriter
ClusteredNeuroVec | ClusteredNeuroVec: Cluster-aware 4D neuroimaging data
ClusteredNeuroVec-class | ClusteredNeuroVec Class
ClusteredNeuroVol | ClusteredNeuroVol Class
ClusteredNeuroVol-class | ClusteredNeuroVol Class
clustered_searchlight | Create a clustered searchlight iterator
cluster_searchlight_series | Cluster-centroid searchlight over cluster time-series
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
cube_shape | Convenience shape generators for 'resampled_searchlight()'
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-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
downsample | Downsample an Image
downsample-method | Downsample an Image
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 --

ecode_name | Get Extension Code Name
ellipsoid_shape | Convenience shape generators for 'resampled_searchlight()'
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
extension | Get Extension by Code
extension-method | Get Extension by Code
extensions | Get Extensions from an Object
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
get_afni_attribute | Get AFNI Attribute from Extension
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 --

has_extensions | Check if Extensions are Present
has_extensions-method | Check if Extensions are Present
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 --

labels-method | Get Labels from ClusteredNeuroVec
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
list_afni_attributes | List AFNI Attributes in Extension
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 --

make_time_weights | Build smooth time weights from motion/outlier metrics
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
mapToColors | Map intensity values to colors
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
mask | Extract Mask from Neuroimaging Object
mask-method | Extract Mask from Neuroimaging Object
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
meta_info | Lightweight metadata for neuroimaging files
meta_info-method | Lightweight metadata for neuroimaging files

## -- 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-downsample | Downsampling Methods for Neuroimaging Objects
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
NiftiExtension | Create a NIfTI Extension
NiftiExtension-class | NiftiExtension Class
NiftiExtensionCodes | Known NIfTI Extension Codes
NiftiExtensionList-class | NiftiExtensionList Class
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 --

parse_afni_extension | Parse AFNI Extension
parse_extension | Parse NIfTI Extension Data
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
plot_montage | Plot a montage of axial (or any-plane) slices using facetting
plot_ortho | Orthogonal three-plane view with optional crosshairs
plot_overlay | Composite an overlay map on a structural background
POST_ANT | Pre-defined anatomical axes
prepare_confounds | Prepare weighted nuisance projectors for each run

## -- 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_image | read_image
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
resampled_searchlight | Create a resampled searchlight iterator
resample_to | Resample an image with readable method names
resolve_cmap | Neuroimaging color palettes and helpers
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_fill_neuro | A ggplot2 fill scale with neuroimaging-friendly defaults
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
searchlight_shape_functions | Convenience shape generators for 'resampled_searchlight()'
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 | NiftiExtension Class
show-method | NiftiExtensionList Class
show-method | Show method for NamedAxis objects
simulate_fmri | Simulate fMRI Data
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 Methods for Neuroimaging Objects
Summary-methods | Summary Methods for Neuroimaging Objects
SUP_INF | Pre-defined anatomical axes

## -- T --

theme_neuro | A minimal, publication-friendly theme for image slices
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.
vec_from_vols | Create NeuroVec from list of NeuroVol objects
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 | [[