neuroim20.8.1 package

AbstractSparseNeuroVec Class

Add a Dimension to an Object

Create AFNI Format Metadata Object

Pre-defined anatomical axes

Arithmetic Operations

Arithmetic Operations for NeuroVec and NeuroVol

Arithmetic Operations for NeuroVol and NeuroVec

This function performs arithmetic operations on two ROIVol objects.

ArrayLike3D Class

ArrayLike4D Class

ArrayLike5D Class

Construct a Minimal NIfTI-1 Header from a NeuroVol

Convert ClusteredNeuroVol to DenseNeuroVol

Convert DenseNeuroVol to array

Coerce ROIVol to DenseNeuroVol using as.dense method

Convert to dense representation

Convert FileBackedNeuroVec to List

as.logical

Convert NeuroVol to a mask

Convert to a LogicalNeuroVol

convert a NeuroVec to a matrix

Generic as.matrix Method

Convert SparseNeuroVol to numeric

Generic Method for Converting Objects to Raster Format

conversion from NeuroVol to LogicalNeuroVol

Convert DenseNeuroVec to sparse representation using mask

Convert to from dense to sparse representation

Extract Image Axes

AxisSet

AxisSet1D

AxisSet2D

AxisSet3D Class

AxisSet4D Class

AxisSet5D Class

BigNeuroVec Class

Create a Memory-Mapped Neuroimaging Vector

Apply a bilateral filter to a volumetric image

BinaryReader Class

Create Binary Reader Object

BinaryWriter Class

Create Binary Writer Object

Create a bootstrap spherical searchlight iterator

Extract Spatial Bounds of an Image

return the centroid of an object

Return a matrix of centroids of an object

Close a BinaryReader or BinaryWriter

Create a clustered searchlight iterator

ClusteredNeuroVol Class

ColumnReader

Create Column Reader Object

Comparison Operations

Concatenate two objects in the time dimension

Extract Connected Components from a 3D Binary Mask

Connected components

convert n-dimensional real world coordinates to grid coordinates

convert n-dimensional real world coordinates to 1D indices

Extract Coordinates from an IndexLookupVol Object

Extract coordinates from an object

Create an Empty NIfTI-1 Header List

Create A Cuboid Region of Interest

Generic function to test whether a file name conforms to the given a `...

Generic function to get the name of the data file, given a file name a...

Create Data Reader for AFNI Format

Create a Data Reader

DenseNeuroVec Class

DenseNeuroVol Class

Get the length of a given dimension of an object

Get Dimensions of FileMetaInfo Object

Drop a Dimension from an Object

Drop a dimension

Generic Drop Method

Generic function to position kernel in a position in image space

Extract or replace parts of an object

Array-like access for 3-dimensional data structures

Array-like access for 4-dimensional data structures

Generic function to test whether a file name conforms to the given `Fi...

FileBackedNeuroVec Class

Create a File-Backed Neuroimaging Vector

FileFormat Class

File Format Operations for Neuroimaging Data

FileMetaInfo Class

FileSource Class

Find 3D anatomical orientation from axis abbreviations

Gaussian Blur for Volumetric Images

Generic function to convert N-dimensional grid coordinates to real wor...

Generic function to convert voxel coordinates in the reference space (...

Generic function to convert N-dimensional grid coordinates to 1D indic...

Edge-Preserving Guided Filter for Volumetric Images

Generic function to test whether a file name conforms to the given `Fi...

Generic function to get the name of the header file, given a file name...

Generic Image Method for Creating Visual Representations

convert 1d indices to n-dimensional real world coordinates

Convert 1d indices to n-dimensional grid coordinates

IndexLookupVol Class

Get Indices from an IndexLookupVol Object

Extract indices

Extract inverse image coordinate transformation

Kernel

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

Laplacian Enhancement Filter for Volumetric Images

Get length of NeuroVec object

Linear Access Method for FileBackedNeuroVec

Extract values from an array-like object using linear indexing.

Load image data from a NeuroVecSource object

Read data from a data source.

LogicalNeuroVol Class

Lookup Values in an IndexLookupVol Object

Index Lookup operation

Map Values from One Set to Another Using a User-supplied Lookup Table

Apply a function to an object.

MappedNeuroVec Class

MappedNeuroVecSource Class

Extract values from a 4D tensor using a matrix of time-space indices.

Convert a Transformation Matrix to a Quaternion Representation

MetaInfo Class

Create Neuroimaging Metadata Object

NamedAxis

Get number of dimensions in axis set

Extract the number of dimensions of an object

Arithmetic and Comparison Operations for Neuroimaging Objects

Resampling Methods for Neuroimaging Objects

NeuroBucket

NeuroHyperVec Class

Constructor for NeuroHyperVec class

neuroim2: neuroimaging data structures for analysis

NeuroObj Class

NeuroSlice Class

NeuroSlice: 2D Neuroimaging Data Container

NeuroSpace Class

NeuroSpace: Spatial Reference System for Neuroimaging Data

NeuroVec Class

NeuroVecSeq Class

Extract Element from NeuroVecSeq

NeuroVecSeq: A Container for Sequential NeuroVec Objects

NeuroVecSource Class

NeuroVecSource

NeuroVol Class

NeuroVol: 3D Neuroimaging Volume Class

Constructor for NeuroVolSource

Create NIFTI Format Metadata Object

Pre-defined null axis

Pre-defined null axis set

Number of Clusters

numericOrMatrix Union

Pre-defined 2D orientation configurations

Pre-defined 3D orientation configurations

Extract Image Origin

Partition an image into a set of disjoint clusters

Create a patch set from a NeuroVol object

Generate a set of coordinate "patches" of fixed size from an image obj...

Get permutation matrix from axis set

Get permutation matrix from axis set

Extract permutation matrix associated with an image

Plot a NeuroSlice

Convert Quaternion Parameters to a Transformation Matrix

Create a spherical random searchlight iterator

Read a set of column vector from an input source (e.g. ColumnReader)

Read Elements from Binary Reader

Read a sequence of elements from an input source

read header information of an image file

Generic function to read image meta info given a file

read_vec

read_vol_list

Load an image volume from a file

Remap the grid-to-world coordinates mapping of an image.

Resample an Image to Match the Space of Another Image

ROI

ROICoords

Create ROI Coordinates Object

ROIVec

Create an instance of class ROIVec

ROIVecWindow

ROIVol

Create ROI Volume Object

ROIVolWindow

Generic functions to scale (center and/or normalize by standard deviat...

Generic Scale Method

Create an exhaustive searchlight iterator for voxel coordinates using ...

Searchlight Analysis Methods

Create an exhaustive searchlight iterator

Extract time series from specific voxel coordinates and return as ROI ...

Extract one or more series from object

Series method for NeuroHyperVec

Show method for NamedAxis objects

Extract image slice

Extract an ordered series of 2D slices from a 3D or 4D object

Extract Geometric Properties of an Image

Extract Voxel Dimensions of an Image

SparseNeuroVec Class

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SparseNeuroVecSource Class

Convert SparseNeuroVol to array

SparseNeuroVol Class

Convert SparseNeuroVol to numeric

Spatial Filtering Methods for Neuroimaging Data

Create Multiple Spherical Regions of Interest

Create a Spherical Region of Interest

Cut a vector-valued object into a list of sub-blocks

Cut an object into a list of spatial or spatiotemporal clusters

Fill Disjoint Sets of Values with the Output of a Function

Summarize Subsets of an Object by Splitting by Row and Applying a Summ...

Center and/or Scale Row-subsets of a Matrix or Matrix-like Object

Create a square region of interest

Generic function to strip extension from file name, given a `FileForma...

Generic function to extract a sub-vector from a NeuroVec object.

Extractor Method for AbstractSparseNeuroVec

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Summary method for Neuroimaging objects

Time axis

Time axis set

Extract image coordinate transformation

Extract Data Values of an Object

Extract an ordered list of 1D vectors.

Extract an ordered series of 3D volumes.

extract voxel coordinates

Find Dimensions of a Given Axis

Write a sequence of elements from an input source

Write a 4d image vector to disk

Write a 3d image volume to disk