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neuroim (version 0.0.6)

Data Structures and Handling for Neuroimaging Data

Description

A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.

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Install

install.packages('neuroim')

Monthly Downloads

165

Version

0.0.6

License

GPL (>= 2)

Maintainer

Bradley Buchsbaum

Last Published

January 7th, 2016

Functions in neuroim (0.0.6)

Generic function to extract the spatial bounds (origin + dim * spacing) of an image param x the object

NIMLSurfaceDataMetaInfo

Constructor for NIMLSurfaceDataMetaInfo class

IndexLookupVolume-class

IndexLookupVolume

BaseMetaInfo-class

AFNIFileDescriptor-class

AFNIFileDescriptor

BaseSource-class

NullMetaInfo-class

FileMetaInfo-class

AxisSet3D-class

BinaryReader-class

FreesurferSurfaceGeometryMetaInfo-class

FreeSurferSurfaceGeometryMetaInfo This class contains meta information for brain surface geometry

Constructor function for BrainSpace class

ROIVolume-class

AxisSet1D-class

BrainSurfaceVector-class

BrainSurfaceVector

BrainVolumeSource-class

BrainVolume BrainVolumeSource A class is used to produce a BrainVolume instance

DenseBrainVector-class

DenseBrainVector

AxisSet5D-class

FreesurferAsciiSurfaceFileDescriptor-class

FresurferAsciiSurfaceFileDescriptor

BrainSpace-class

BrainVectorSource-class

BrainVectorSource

Generic function to drop a dimension from an object

Generic function to convert N-dimensional real world coordinates to 1D indices

BrainSlice-class

show,NullMetaInfo-method

show a NullMetaInfo

Generic getter to extract image origin

Generic function to load data from a data source

ColumnReader-class

ClusteredBrainVolume-class

ClusteredBrainVolume

AxisSet4D-class

Generic function to add a dimension to an object

close,BinaryReader-method

mergePartitions

mergePartitions

BrainData-class

RandomSearchlight

Create an Random Searchlight iterator

Create a Kernel object

Create an instance of class ROIVolume

BrainSurfaceVectorSource-class

BrainSurfaceVectorSource

BrainBucketSource-class

BrainBucketSource

Load an image volume from a file

[,SparseBrainVolume,missing,missing,ANY-method

BootstrapSearchlight

Create a searchlight iterator that samples regions from within a mask. Searchlight centers are sampled *without* replacement, but the same voxel can belong to multiple searchlight samples. It is in the latter sense that this is a bootstrap resampling scheme.

BrainBucket-class

BrainVectorSource

BrainVectorSource

Generic function to convert N-dimensional real world coordinates to grid coordinates

BrainVector-class

Extract connected components from a 3D mask

SurfaceDataMetaInfo

Constructor for SurfaceDataMetaInfo class

BrainFileSource-class

BrainFileSource Base class for representing a data source for images. The purpose of this class is to provide a layer in between low level IO and image loading functionality.

BrainSurfaceSource-class

BrainSurfaceSource

NIMLSurfaceFileDescriptor-class

NIMLSurfaceFileDescriptor

BrainFileDescriptor-class

BrainFileDescriptor

as.list,SparseBrainVector-method

overlay two objects

BrainSource-class

Generic function to map values from one set to another using a user-supplied lookup table

image,BrainVolume-method

show,AxisSet1D-method

show an AxisSet1D

BinaryWriter-class

BrainSlice constructor

SurfaceDataMetaInfo-class

SurfaceDataMetaInfo This class contains meta information for surface-based data (the values that map to a surface geometry)

print,AxisSet3D-method

print a AxisSet3D instance

as.logical,BrainVolume-method

headerFileMatches

Generic function to test whether a file name conforms to the given BrainFileDescriptor instance. Will test for match to header file only

AxisSet2D-class

given three named axes return AxisSet3D singleton

dim,FileMetaInfo-method

dim of FileMetaInfo

[[,BrainBucket,index,missing-method

extract labeled volume from BrainBucket

Concatenate two objects

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

SparseBrainVolume-class

SparseBrainVolume

NamedAxis-class

[,SparseBrainVector,numeric,missing,ANY-method

Extract coordinates

as.numeric,SparseBrainVolume-method

Convert SparseBrainVolume to numeric

LogicalBrainVolume-class

LogicalBrainVolume

Create a square region of interest where the z-dimension is fixed at one voxel coordinate.

Generic function to extract the number of dimensions of an object

NIfTIFileDescriptor-class

NIfTIFileDescriptor

Create A Cuboid Region of Interest

SparseBrainVector-class

SparseBrainVector

[,SparseBrainVolume,numeric,missing,missing-method

dataFileMatches

Generic function to test whether a file name conforms to the given a BrainFileDescriptor instance. Will test for match to data file only

Generic function to convert N-dimensional grid coordinate coordinates to real world coordinates Generic function to convert N-dimensional grid coordinates to real world coordinates

length,ROIVolume-method

Get length of BrainVector. This is the numbe rof volumes in the volume vector (e.g. the 4th image dimension)

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

Constructor for NIfTIMetaInfo class

Create an exhaustive searchlight iterator

show,AxisSet3D-method

show an AxisSet3D

DenseBrainVolume-class

DenseBrainVolume

SurfaceGeometryMetaInfo

Constructor for SurfaceGeometryMetaInfo class

show,NamedAxis-method

show an NamedAxis

[,SparseBrainVolume,matrix,missing,ANY-method

conversion from DenseBrainVolume to array

Generic function to extract a set of series from a 4D image

[,SparseBrainVector,missing,missing,ANY-method

show,SurfaceGeometryMetaInfo-method

show an SurfaceGeometryMetaInfo

as.matrix,SparseBrainVector-method

as.raster,Layer-method

dim,BrainSpace-method

NIMLSurfaceDataMetaInfo-class

NIMLSurfaceDataMetaInfo This class contains meta information for surface-based data for the NIML data format

BrainMetaInfo-class

BrainMetaInfo This class contains meta information from an image

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

extract voxel coordinates

Generic function to convert N-dimensional grid coordinate to 1D indices

Create A Spherical Region of Interest

Generic getter function to extract image axes

Index Lookup operation

print,NamedAxis-method

print a NamedAxis

Render a slice at z coordinate

print,AxisSet2D-method

print a AxisSet2D instance

[,SparseBrainVolume,numeric,numeric,ANY-method

[,ROIVolume,numeric,missing,ANY-method

extract data from ROIVolume

Generic function to apply a function to an object

show,BrainVolume-method

show a BrainVolume

as.vector,BrainData-method

convert BrainData instance to vector

BrainVolume-class

Base class for image representing 3D volumetric data.

BrainSurface-class

Generic function to create data reader

read header information of an image file

Convert to a LogicalBrainVolume

Generic function to extract a one or more individual volumes from a four-dimensional image

Convert to from dense to sparse representation

Generic functions to apply a function to each (2D) slice of an image

Generic function to center/scale row-subsets of a matrix or matrix-like object

show,AxisSet2D-method

show an AxisSet2D

show,SparseBrainVector-method

show a SparseBrainVector

Generic functions to apply a function to each series of a 4D image That is, if the 4th dimension is 'time' each series is a 1D time series.

Generic function to read a sequence of elements from an input source

Generic function to test whether a file name conforms to the given BrainFileDescriptor instance. Will test for match to either header file or data file

Extract indices

show,BaseMetaInfo-method

show a BaseMetaInfo

matrixToVolumeList

matrixToVolumeList converts a matrix to a list of BrainVolumes with values filled at grid coordinates determined by the vox argument.

show,BrainVector-method

show a BrainVector

show,BrainVectorSource-method

show a BrainVectorSource

Generic getter to extract image coordinate transformation

SurfaceGeometryMetaInfo-class

SurfaceGeometryMetaInfo This class contains meta information for brain surface geometry

load an surface from a set of files

Generic function to convert 1-dimensional real axis coordinates along a single axis dimension to an 1D index along the same axis

Generic function to convert 1D indices to N-dimensional grid coordinates

Generic function to extract geometric properties of an image.

SparseBrainVectorSource-class

SparseBrainVectorSource

Extract vector series from object

[,BrainBucket,index,missing,ANY-method

extract labeled volume from BrainBucket

show,SurfaceDataMetaInfo-method

show an SurfaceDataMetaInfo

load Freesurfer ascii surface

[,SparseBrainVector,missing,numeric,ANY-method

show,AxisSet4D-method

show an AxisSet4D

[,SparseBrainVector,numeric,numeric,ANY-method

Generic function to write a 3D image volume to disk

show,ROIVolume-method

show an ROIVolime

Extract a 2D slice from an image volume

Render an image to create a drawable image.

Find connected components

Generic function to apply a function to each volume of a four-dimensional image

as.array,BrainData-method

convert BrainData instance to array

Generic function to read image meta info given a file and a BrainFileDescriptor instance.

show,BrainSpace-method

show a BrainSpace

Generic function to strip extension from file name, given a BrainFileDescriptor instance.

Generic function to write a 4D image vector to disk

given two named axes return AxisSet2D singleton

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.

names,BrainBucketSource-method

dim,BrainData-method

dim of BrainData object

as.matrix,BrainData-method

convert BrainData instance to matrix

Generic function to fill disjoint sets of values with the output of a function

Generic function to extract data values of object

Generic function to write a sequence of elements from an input source

Generic function to print an object

Generic function to extract the voxel dimensions of an image

Generic getter to extract inverse image coordinate transformation

Extract permutation matrix

show,FileMetaInfo-method

show a FileMetaInfo

Generic function to convert 1D indices to N-dimensional real world coordinates

Generic function to read a set of column vector from an input source (e.g. ColumnReader)

[,SparseBrainVolume,missing,numeric,ANY-method

Generic function to summarize subsets of an object by first splitting by row and then "reducing" by a summary function