AbstractSparseNeuroVec-class
                        AbstractSparseNeuroVec Class
Arith,NeuroVec,NeuroVol-method
                        Arithmetic Operations for NeuroVec and NeuroVol
Arith,NeuroVol,NeuroVec-method
                        Arithmetic Operations for NeuroVol and NeuroVec
Arith,ROIVol,ROIVol-method
                        This function performs arithmetic operations on
                        two ROIVol objects.
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
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
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
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,SparseNeuroVec-method
                        Summary method for Neuroimaging objects
TIME                    Time axis
TimeAxis                Time axis set
[                       Extract or replace parts of an object
[,AbstractSparseNeuroVec,numeric,numeric,ANY-method
                        Extractor Method for AbstractSparseNeuroVec
[[,NeuroVec,numeric-method
                        [[
[[,NeuroVecSeq,numeric-method
                        Extract Element from NeuroVecSeq
[[,SparseNeuroVec,numeric-method
                        [[
add_dim                 Add a Dimension to an Object
anatomical_axes         Pre-defined anatomical axes
as                      conversion from 'NeuroVol' to 'LogicalNeuroVol'
as-ClusteredNeuroVol-DenseNeuroVol
                        Convert ClusteredNeuroVol to DenseNeuroVol
as.dense                Convert to dense representation
as.dense,ClusteredNeuroVol-method
                        Coerce ROIVol to DenseNeuroVol using as.dense
                        method
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,MappedNeuroVec-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_nifti_header         Construct a Minimal NIfTI-1 Header from a
                        NeuroVol
axes                    Extract Image Axes
bilateral_filter        Apply a bilateral filter to a volumetric image
bootstrap_searchlight   Create a bootstrap spherical searchlight
                        iterator
bounds                  Extract Spatial Bounds of an Image
centroid                return the centroid of an object
centroids               Return a matrix of centroids of an object
close,BinaryReader-method
                        Close a BinaryReader or BinaryWriter
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
dim,FileMetaInfo-method
                        Get Dimensions of FileMetaInfo Object
dim_of                  Get the length of a given dimension of an
                        object
drop                    Generic Drop Method
drop,NeuroVec-method    Drop a dimension
drop_dim                Drop a Dimension from an Object
embed_kernel            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
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
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
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
laplace_enhance         Laplacian Enhancement Filter for Volumetric
                        Images
length,NeuroVec-method
                        Get length of NeuroVec object
linear_access           Extract values from an array-like object using
                        linear indexing.
linear_access,FileBackedNeuroVec,numeric-method
                        Linear Access Method for FileBackedNeuroVec
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
map_values              Map Values from One Set to Another Using a
                        User-supplied Lookup Table
mapf                    Apply a function to an 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
ndim                    Extract the number of dimensions of an object
ndim,AxisSet-method     Get number of dimensions in axis set
neuro-ops               Arithmetic and Comparison Operations for
                        Neuroimaging Objects
neuro-resample          Resampling Methods for Neuroimaging Objects
neuroim2-package        neuroim2: neuroimaging data structures for
                        analysis
num_clusters            Number of Clusters
numericOrMatrix-class   numericOrMatrix Union
origin                  Extract Image Origin
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
perm_mat,AxisSet2D-method
                        Get permutation matrix from axis set
perm_mat,AxisSet3D-method
                        Get permutation matrix from axis set
plot,NeuroSlice-method
                        Plot a NeuroSlice
quaternToMatrix         Convert Quaternion Parameters to a
                        Transformation Matrix
random_searchlight      Create a spherical random searchlight iterator
read_elements,BinaryReader,numeric-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_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.
resample                Resample an Image to Match the Space of Another
                        Image
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.
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,NeuroHyperVec,ANY-method
                        Series method for NeuroHyperVec
series_roi              Extract time series from specific voxel
                        coordinates and return as ROI object
show,NamedAxis-method   Show method for NamedAxis objects
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
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_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          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
