AbstractSparseNeuroVec-class
                        AbstractSparseNeuroVec Class
Arith-methods           Arithmetic Operations
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             Create a Memory-Mapped Neuroimaging Vector
BigNeuroVec-class       BigNeuroVec Class
BinaryReader            Create Binary Reader Object
BinaryReader-class      BinaryReader Class
BinaryWriter            Create Binary Writer Object
BinaryWriter-class      BinaryWriter Class
ClusteredNeuroVec       ClusteredNeuroVec: Cluster-aware 4D
                        neuroimaging data
ClusteredNeuroVec-class
                        ClusteredNeuroVec Class
ClusteredNeuroVol-class
                        ClusteredNeuroVol Class
ColumnReader            Create Column Reader Object
ColumnReader-class      ColumnReader
Compare-methods         Comparison Operations
DenseNeuroVec-class     DenseNeuroVec Class
DenseNeuroVol-class     DenseNeuroVol Class
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
IndexLookupVol-class    IndexLookupVol Class
Kernel                  Create a Kernel object from a function of
                        distance from kernel center
Kernel-class            Kernel
Logic-methods           Logic Operations for Neuroimaging Volumes
LogicalNeuroVol-class   LogicalNeuroVol Class
MappedNeuroVec-class    MappedNeuroVec Class
MappedNeuroVecSource-class
                        MappedNeuroVecSource Class
MetaInfo                Create Neuroimaging Metadata Object
MetaInfo-class          MetaInfo Class
NIFTIMetaInfo           Create NIFTI Format Metadata Object
NamedAxis-class         NamedAxis
NeuroBucket-class       NeuroBucket
NeuroHyperVec           Constructor for NeuroHyperVec class
NeuroHyperVec-class     NeuroHyperVec Class
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-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
None                    Pre-defined null axis
NullAxis                Pre-defined null axis set
OrientationList2D       Pre-defined 2D orientation configurations
OrientationList3D       Pre-defined 3D orientation configurations
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
SparseNeuroVec-class    SparseNeuroVec Class
SparseNeuroVecSource-class
                        SparseNeuroVecSource Class
SparseNeuroVol-class    SparseNeuroVol Class
Summary-methods         Summary Methods for Neuroimaging Objects
TIME                    Time axis
TimeAxis                Time axis set
[,DenseNeuroVol,numeric,missing,ANY-method
                        [[
[[,AbstractSparseNeuroVec,numeric-method
                        [[
[[,NeuroVecSeq,numeric-method
                        Extract Element from NeuroVecSeq
add_dim                 Add a Dimension to an Object
affine_utils            Affine utility functions
anatomical_axes         Pre-defined anatomical axes
annotate_orientation    Add L/R and A/P/S/I annotations (optional)
as-ClusteredNeuroVol-DenseNeuroVol
                        Convert ClusteredNeuroVol to DenseNeuroVol
as.array                Generic as.array Method
as.array,ClusteredNeuroVol-method
                        Convert ClusteredNeuroVol to a base array
as.dense                Convert to dense representation
as.dense,ClusteredNeuroVol-method
                        Convert a NeuroVecSeq to a DenseNeuroVec
as.list,FileBackedNeuroVec-method
                        Convert FileBackedNeuroVec to List
as.logical,NeuroVol-method
                        as.logical
as.mask                 Convert to a LogicalNeuroVol
as.mask,NeuroVol,missing-method
                        Convert NeuroVol to a mask
as.matrix               Generic as.matrix Method
as.matrix,ClusteredNeuroVec-method
                        convert a 'NeuroVec' to a matrix
as.numeric,SparseNeuroVol-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,DenseNeuroVec,LogicalNeuroVol-method
                        Convert DenseNeuroVec to sparse representation
                        using mask
as.vector,SparseNeuroVol-method
                        Convert SparseNeuroVol to a base vector
as_canonical            Reorient Image to Canonical (RAS+) Orientation
as_mmap                 Convert a NeuroVec to a memory-mapped
                        representation
as_nifti_header         Construct a Minimal NIfTI-1 Header from a
                        NeuroVol
axcodes                 Get Orientation Axis Codes
axes                    Extract Image Axes
bilateral_filter        Apply a bilateral filter to a volumetric image
bilateral_filter_4d     Apply a 4D bilateral filter to a NeuroVec
bounds                  Extract Spatial Bounds of an Image
centroid                return the centroid of an object
centroids               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,BinaryReader-method
                        Close a BinaryReader or BinaryWriter
cluster_searchlight_series
                        Cluster-centroid searchlight over cluster
                        time-series
clustered_searchlight   Create a clustered searchlight iterator
concat                  Concatenate two objects in the time dimension
conn_comp               Connected components
conn_comp_3D            Extract Connected Components from a 3D Binary
                        Mask
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                  Extract coordinates from an object
coords,IndexLookupVol-method
                        Extract Coordinates from an IndexLookupVol
                        Object
createNIfTIHeader       Create an Empty NIfTI-1 Header List
cuboid_roi              Create A Cuboid Region of Interest
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
data_reader,NIFTIMetaInfo-method
                        Create Data Reader for AFNI Format
deoblique               Deoblique a Neuroimaging Space or Volume
dim,ClusteredNeuroVec-method
                        Get Dimensions of FileMetaInfo Object
dim_of                  Get the length of a given dimension of an
                        object
downsample              Downsample an Image
drop                    Generic Drop Method
drop,NeuroVec-method    Drop a dimension
drop_dim                Drop a Dimension from an Object
ecode_name              Get Extension Code Name
embed_kernel            Generic function to position kernel in a
                        position in image space
extension               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
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
findAnatomy3D           Find 3D anatomical orientation from axis
                        abbreviations
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_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
                        coordinates to 1D indices
guided_filter           Edge-Preserving Guided Filter for Volumetric
                        Images
has_extensions          Check if Extensions are Present
header                  Access NIfTI Header Information
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
image                   Generic Image Method for Creating Visual
                        Representations
index_to_coord          convert 1d indices to n-dimensional real world
                        coordinates
index_to_grid           Convert 1d indices to n-dimensional grid
                        coordinates
indices                 Extract indices
indices,IndexLookupVol-method
                        Get Indices from an IndexLookupVol Object
inverse_trans           Extract inverse image coordinate transformation
labels,ClusteredNeuroVec-method
                        Get Labels from ClusteredNeuroVec
laplace_enhance         Laplacian Enhancement Filter for Volumetric
                        Images
length,ClusteredNeuroVec-method
                        Get length of NeuroVec object
linear_access           Extract values from an array-like object using
                        linear indexing.
linear_access,DenseNeuroVol,numeric-method
                        Linear Access Method for FileBackedNeuroVec
list_afni_attributes    List AFNI Attributes in Extension
load_data,MappedNeuroVecSource-method
                        Load image data from a NeuroVecSource object
lookup                  Index Lookup operation
lookup,IndexLookupVol,numeric-method
                        Lookup Values in an IndexLookupVol Object
make_time_weights       Build smooth time weights from motion/outlier
                        metrics
mapToColors             Map intensity values to colors
map_values              Map Values from One Set to Another Using a
                        User-supplied Lookup Table
mapf                    Apply a function to an object.
mask                    Extract Mask from Neuroimaging Object
matricized_access       Extract values from a 4D tensor using a matrix
                        of time-space indices.
matrixToQuatern         Convert a Transformation Matrix to a Quaternion
                        Representation
mean-methods            Temporal Mean of a NeuroVec
meta_info               Lightweight metadata for neuroimaging files
ndim                    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
neuroim2-package        neuroim2: neuroimaging data structures for
                        analysis
not-methods             Logical Negation for Neuroimaging Volumes
num_clusters            Number of Clusters
numericOrMatrix-class   numericOrMatrix Union
orientation_utils       Orientation utility functions
origin                  Extract Image Origin
parse_afni_extension    Parse AFNI Extension
parse_extension         Parse NIfTI Extension Data
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.
patch_set,NeuroVol,numeric,missing-method
                        Create a patch set from a NeuroVol object
perm_mat                Extract permutation matrix associated with an
                        image
plot,NeuroSlice-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
prepare_confounds       Prepare weighted nuisance projectors for each
                        run
quaternToMatrix         Convert Quaternion Parameters to a
                        Transformation Matrix
random_searchlight      Create a spherical random searchlight iterator
read_header             read header information of an image file
read_hyper_vec          Read a 5D image as a NeuroHyperVec
read_image              read_image
read_meta_info          Generic function to read image meta info given
                        a file
read_vec                read_vec
read_vol                Load a single 3D image volume from a file
read_vol_list           read_vol_list
reorient                Remap the grid-to-world coordinates mapping of
                        an image.
resample                Resample an Image to Match the Space of Another
                        Image
resample_to             Resample an image with readable method names
resampled_searchlight   Create a resampled searchlight iterator
resolve_cmap            Neuroimaging color palettes and helpers
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.
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_roi              Extract time series from specific voxel
                        coordinates and return as ROI object
show,NamedAxis-method   Show method for NamedAxis objects
simulate_fmri           Simulate fMRI Data
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
space_utils             Space utility functions
spacing                 Extract Voxel Dimensions of an Image
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_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
square_roi              Create a square region of interest
strip_extension         Generic function to strip extension from file
                        name, given a 'FileFormat' instance.
sub_clusters            Select a Subset of Clusters
sub_vector              Generic function to extract a sub-vector from a
                        'NeuroVec' object.
summary-neuro-methods   Summary of Neuroimaging Objects
temporal_access         Extract full sparse rows across time.
theme_neuro             A minimal, publication-friendly theme for image
                        slices
trans                   Extract image coordinate transformation
values                  Extract Data Values of an Object
vec_from_vols           Create NeuroVec from list of NeuroVol objects
vectors                 Extract an ordered list of 1D vectors.
vols                    Extract an ordered series of 3D volumes.
volume_labels           Get per-volume labels for a 'NeuroVec'.
voxels                  extract voxel coordinates
which_dim               Find Dimensions of a Given Axis
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
