Package: neuroim 0.1.0
neuroim: Data Structures and Handling for Neuroimaging Data
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.
Authors:
neuroim_0.1.0.tar.gz
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neuroim.pdf |neuroim.html✨
neuroim/json (API)
| # Install 'neuroim' in R: |
| install.packages('neuroim', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bbuchsbaum/neuroim/issues
Datasets:
- MNI_SPACE_1MM - MNI SPACE 1MM
Last updated 4 years agofrom:a0c2c5db6e. Checks:OK: 1 ERROR: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 07 2024 |
| R-4.5-win-x86_64 | ERROR | Sep 07 2024 |
| R-4.5-linux-x86_64 | ERROR | Sep 07 2024 |
| R-4.4-win-x86_64 | ERROR | Sep 07 2024 |
| R-4.4-mac-x86_64 | ERROR | Sep 07 2024 |
| R-4.4-mac-aarch64 | ERROR | Sep 07 2024 |
| R-4.3-win-x86_64 | ERROR | Sep 07 2024 |
| R-4.3-mac-x86_64 | ERROR | Sep 07 2024 |
| R-4.3-mac-aarch64 | ERROR | Sep 07 2024 |
Exports:addDimAFNIMetaInfoas.arrayas.listas.maskas.matrixas.sparseaxesaxisToIndexBasisBrainVectorBinaryReaderBinaryWriterBootstrapSearchlightboundsBrainBucketBrainBucketSourceBrainMetaInfoBrainSliceBrainSpaceBrainVectorBrainVectorSourceBrainVolumeBrainVolumeSourcecloseClusteredBrainVolumeClusteredSearchlightColumnReaderconcatconnCompconnComp3DcoordscoordToGridcoordToIndexdataFiledataFileMatchesdataReaderDenseBrainVectorDenseBrainVolumedropDimeachSerieseachSliceeachVolumefileMatchesfillgridToCoordgridToGridgridToIndexheaderFileheaderFileMatchesimageIndexLookupVolumeindexToAxisindexToCoordindexToGridindicesinverseTransKernelloadBucketloadDataloadVectorloadVolumeloadVolumeListLogicalBrainVolumelookupmakeVectormakeVolumemapmapToColorsmatchAnatomy2DmatchAnatomy3DmatrixToVolumeListndimNIfTIMetaInfonumClustersoriginoverlaypermMatprintRandomSearchlightreadColumnsreadElementsreadHeaderreadMetaInfoRegionCubeRegionSphereRegionSquarerenderreorientROIVectorROIVolumescaleSeriesSearchlightseriesseries_roiseriesItershowslicesliceDataspacespacingSparseBrainVectorSparseBrainVectorSourceSparseBrainVolumesplitFillsplitReducesplitScalestripExtensionsubVectortakeVolumetransvaluesvoxelswriteElementswriteVectorwriteVolume
Dependencies:abindassertthatclicpp11gluehashigraphiteratorslatticelifecyclemagrittrMatrixmmappkgconfigplyrRcppRcppArmadillorflannrlangRNiftistringistringrvctrs
Regions of Interest
Rendered fromregionOfInterest.Rmdusingknitr::rmarkdownon Sep 07 2024.Last update: 2015-06-22
Started: 2014-05-28
The neuroim package
Rendered fromneuroim.Rmdusingknitr::rmarkdownon Sep 07 2024.Last update: 2015-06-22
Started: 2014-05-28
Working with Image Volumes
Rendered fromFileIO.Rmdusingknitr::rmarkdownon Sep 07 2024.Last update: 2015-06-20
Started: 2015-06-20
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| extract labeled volume from 'BrainBucket' | [,BrainBucket,index,missing,ANY-method |
| subset an 'ROIVolume' | [,ROIVolume,logical,missing,ANY-method [,ROIVolume,numeric,missing,ANY-method |
| extractor | [,SparseBrainVector,missing,missing,ANY-method |
| extractor | [,SparseBrainVector,missing,numeric,ANY-method |
| extractor | [,SparseBrainVector,numeric,missing,ANY-method |
| extractor | [,SparseBrainVector,numeric,numeric,ANY-method |
| extractor | [,SparseBrainVolume,matrix,missing,ANY-method |
| extractor | [,SparseBrainVolume,missing,missing,ANY-method |
| extractor | [,SparseBrainVolume,missing,numeric,ANY-method |
| extractor | [,SparseBrainVolume,numeric,missing,missing-method |
| extractor | [,SparseBrainVolume,numeric,numeric,ANY-method |
| extract labeled volume from 'BrainBucket' | [[,BrainBucket,index,missing-method |
| extractor | [[,BrainVector,numeric,ANY-method [[,SparseBrainVector,numeric,ANY-method |
| Generic function to add a dimension to an object | addDim addDim,BrainSpace,numeric-method |
| AFNIFileDescriptor | AFNIFileDescriptor-class |
| AFNIMetaInfo | AFNIMetaInfo |
| conversion from DenseBrainVolume to array | as |
| convert 'BrainData' instance to array | as.array,BrainData-method |
| as.list | as.list,BrainVector-method as.list,SparseBrainVector-method |
| as.logical | as.logical,BrainVolume-method |
| Convert to a LogicalBrainVolume | as.mask as.mask,BrainVolume,missing-method as.mask,BrainVolume,numeric-method |
| convert 'BrainData' instance to matrix | as.matrix,BrainData-method |
| convert a 'ROIVector' to a matrix | as.matrix,DenseBrainVector-method as.matrix,ROIVector-method as.matrix,SparseBrainVector-method |
| Convert SparseBrainVolume to numeric | as.numeric,SparseBrainVolume-method |
| Convert to from dense to sparse representation | as.sparse as.sparse,DenseBrainVector,LogicalBrainVolume-method as.sparse,DenseBrainVector,numeric-method as.sparse,DenseBrainVolume,LogicalBrainVolume-method as.sparse,DenseBrainVolume,numeric-method |
| convert 'BrainData' instance to vector | as.vector,BrainData-method |
| Generic getter function to extract image axes | axes axes,BrainData-method axes,BrainSpace-method |
| Base | AxisSet-class |
| AxisSet1D | AxisSet1D-class |
| AxisSet2D | AxisSet2D-class |
| AxisSet3D | AxisSet3D-class |
| AxisSet4D | AxisSet4D-class |
| AxisSet5D | AxisSet5D-class |
| Convert 1-dimensional real axis coordinates along a single axis dimension to a 1D index along the same axis. | axisToIndex axisToIndex,BrainSpace,numeric,numeric-method indexToAxis indexToAxis,BrainSpace,numeric,numeric-method |
| Base | Base-class |
| BaseMetaInfo | BaseMetaInfo-class |
| BaseSource | BaseSource-class |
| BasisBrainVector | BasisBrainVector-class |
| BinaryReader | BinaryReader |
| BinaryReader | BinaryReader-class |
| BinaryWriter | BinaryWriter BinaryWriter-class |
| Create a spherical searchlight iterator that samples regions from within a mask. | BootstrapSearchlight |
| Generic function to extract the spatial bounds (origin + dim * spacing) of an image param x the object | bounds bounds,BrainData-method bounds,BrainSpace-method |
| BrainBucket | BrainBucket BrainBucket-class |
| BrainBucketSource | BrainBucketSource BrainBucketSource-class |
| BrainData | BrainData-class |
| BrainFileDescriptor | BrainFileDescriptor-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. | BrainFileSource-class |
| BrainMetaInfo This class contains meta information from an image | BrainMetaInfo BrainMetaInfo-class |
| BrainSlice constructor | BrainSlice |
| BrainSlice | BrainSlice-class |
| BrainSource | BrainSource-class |
| Constructor function for 'BrainSpace' class | BrainSpace |
| BrainSpace | BrainSpace-class |
| BrainVector | BrainVector BrainVector-class |
| BrainVectorSource | BrainVectorSource |
| BrainVectorSource | BrainVectorSource-class |
| BrainVolume | BrainVolume |
| BrainVolume Base class for image representing 3D volumetric data. | BrainVolume-class |
| BrainVolumeSource A class is used to produce a 'BrainVolume' instance | BrainVolumeSource BrainVolumeSource-class |
| close | close,BinaryReader-method close,BinaryWriter-method |
| ClusteredBrainVolume | ClusteredBrainVolume ClusteredBrainVolume-class |
| Create a clustered Searchlight iterator | ClusteredSearchlight |
| ColumnReader | ColumnReader |
| ColumnReader | ColumnReader-class |
| Concatenate two objects | concat concat,BrainVector,BrainVector-method concat,BrainVector,BrainVolume-method concat,BrainVolume,BrainVector-method concat,DenseBrainVolume,DenseBrainVolume-method concat,DenseBrainVolume,missing-method concat,SparseBrainVector,missing-method concat,SparseBrainVector,SparseBrainVector-method |
| Find connected components | connComp connComp,BrainVolume-method |
| Extract connected components from a 3D mask | connComp3D |
| Extract coordinates | coords coords,IndexLookupVolume-method coords,ROIVolume-method coords,SparseBrainVector-method |
| Generic function to convert N-dimensional real world coordinates to grid coordinates | coordToGrid coordToGrid,BrainSpace,matrix-method coordToGrid,BrainSpace,numeric-method coordToGrid,BrainVolume,matrix-method |
| Generic function to convert N-dimensional real world coordinates to 1D indices | coordToIndex coordToIndex,BrainSpace,matrix-method coordToIndex,BrainSpace,numeric-method coordToIndex,BrainVolume,matrix-method |
| Generic function to get the name of the data file, given a file name and a 'BrainFileDescriptor' instance. | dataFile dataFile,BrainFileDescriptor,character-method |
| Generic function to test whether a file name conforms to the given a 'BrainFileDescriptor' instance. Will test for match to data file only | dataFileMatches dataFileMatches,BrainFileDescriptor,character-method |
| Generic function to create data reader | dataReader dataReader,AFNIMetaInfo-method dataReader,NIfTIMetaInfo-method |
| DenseBrainVector | DenseBrainVector DenseBrainVector-class |
| DenseBrainVolume | DenseBrainVolume DenseBrainVolume-class |
| dim of 'BrainData' object | dim,BrainData-method |
| dim | dim,BrainSpace-method |
| dim of 'FileMetaInfo' | dim,FileMetaInfo-method |
| Generic function to drop a dimension from an object | dropDim dropDim,AxisSet2D,missing-method dropDim,AxisSet2D,numeric-method dropDim,AxisSet3D,missing-method dropDim,AxisSet3D,numeric-method dropDim,BrainSpace,missing-method dropDim,BrainSpace,numeric-method |
| 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. | eachSeries eachSeries,BrainVector,function,missing-method eachSeries,DenseBrainVector,function,missing-method eachSeries,SparseBrainVector,function,logical-method |
| Generic functions to apply a function to each (2D) slice of an image | eachSlice eachSlice,BrainVolume,function,logical-method eachSlice,BrainVolume,function,missing-method |
| Generic function to apply a function to each volume of a four-dimensional image | eachVolume eachVolume,BrainBucket,function,logical,ANY-method eachVolume,BrainBucket,function,missing,missing-method eachVolume,BrainVector,function,logical,ANY-method eachVolume,BrainVector,function,missing,BrainVolume-method eachVolume,BrainVector,function,missing,missing-method eachVolume,SparseBrainVector,function,logical,missing-method eachVolume,SparseBrainVector,function,missing,LogicalBrainVolume-method eachVolume,SparseBrainVector,function,missing,missing-method |
| 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 | fileMatches fileMatches,BrainFileDescriptor,character-method |
| FileMetaInfo | AFNIMetaInfo-class FileMetaInfo-class NIfTIMetaInfo-class |
| Generic function to map values from one set to another using a user-supplied lookup table | fill fill,BrainVolume,list-method fill,BrainVolume,matrix-method |
| Generic function to convert N-dimensional grid coordinate coordinates to real world coordinates | gridToCoord gridToCoord,BrainSpace,matrix-method gridToCoord,BrainSpace,numeric-method gridToCoord,BrainVolume,matrix-method |
| Generic function to convert voxel coordinates in the reference space (LPI) to native array space. | gridToGrid gridToGrid,BrainSpace,matrix-method gridToGrid,matrix,matrix-method |
| Generic function to convert N-dimensional grid coordinate to 1D indices | gridToIndex gridToIndex,BrainSlice,matrix-method gridToIndex,BrainSpace,matrix-method gridToIndex,BrainSpace,numeric-method gridToIndex,BrainVolume,matrix-method gridToIndex,BrainVolume,numeric-method |
| Generic function to get the name of the header file, given a file name and a 'BrainFileDescriptor' instance. | headerFile headerFile,BrainFileDescriptor,character-method |
| Generic function to test whether a file name conforms to the given 'BrainFileDescriptor' instance. Will test for match to header file only | headerFileMatches headerFileMatches,BrainFileDescriptor,character-method |
| image | image,BrainVolume-method |
| IndexLookupVolume | IndexLookupVolume IndexLookupVolume-class |
| Generic function to convert 1D indices to N-dimensional real world coordinates | indexToCoord indexToCoord,BrainSpace,numeric-method indexToCoord,BrainVolume,index-method |
| Generic function to convert 1D indices to N-dimensional grid coordinates | indexToGrid indexToGrid,BrainSlice,index-method indexToGrid,BrainSpace,numeric-method indexToGrid,BrainVector,index-method indexToGrid,BrainVector,integer-method indexToGrid,BrainVolume,index-method indexToGrid,BrainVolume,integer-method |
| Extract indices | indices indices,IndexLookupVolume-method indices,ROIVector-method indices,ROIVolume-method indices,SparseBrainVector-method |
| Generic getter to extract inverse image coordinate transformation | inverseTrans inverseTrans,BrainData-method inverseTrans,BrainSpace-method |
| Create a Kernel object from a function of distance from kernel center | Kernel |
| Kernel | Kernel-class |
| Get length of 'BrainVector'. This is the numbe rof volumes in the volume vector (e.g. the 4th image dimension) | length,BrainVector-method length,ROIVolume-method |
| loadBucket | loadBucket |
| Generic function to load data from a data source | loadData loadData,BrainBucketSource-method loadData,BrainVectorSource-method loadData,BrainVolumeSource-method loadData,SparseBrainVectorSource-method |
| loadVector | loadVector |
| Load an image volume from a file | loadVolume |
| loadVolumeList | loadVolumeList |
| LogicalBrainVolume | LogicalBrainVolume LogicalBrainVolume-class |
| Index Lookup operation | lookup lookup,IndexLookupVolume,numeric-method lookup,SparseBrainVector,numeric-method |
| makeVector | makeVector |
| makeVolume | makeVolume |
| Generic function to apply a function to an object | map map,BrainVolume,Kernel-method |
| mapToColors | mapToColors |
| given two named axes return AxisSet2D singleton | matchAnatomy2D |
| given three named axes return AxisSet3D singleton | matchAnatomy3D |
| matrixToVolumeList converts a matrix to a list of BrainVolumes with values filled at grid coordinates determined by the 'vox' argument. | matrixToVolumeList |
| MNI SPACE 1MM | MNI_SPACE_1MM |
| NamedAxis | NamedAxis-class |
| names | names,BrainBucket-method names,BrainBucketSource-method |
| Generic function to extract the number of dimensions of an object | ndim ndim,AxisSet-method ndim,BrainData-method ndim,BrainSpace-method |
| neuroim | neuroim-package neuroim |
| NIfTIFileDescriptor | NIfTIFileDescriptor-class |
| Constructor for 'NIfTIMetaInfo' class | NIfTIMetaInfo |
| NullMetaInfo | NullMetaInfo-class |
| numClusters | numClusters numClusters,ClusteredBrainVolume-method |
| Generic getter to extract image origin | origin origin,BrainData-method origin,BrainSpace-method |
| overlay two objects | overlay |
| patchSet | patchSet |
| Extract permutation matrix | permMat permMat,AxisSet2D-method permMat,AxisSet3D-method permMat,BrainSpace-method |
| Generic function to print an object | |
| print a 'AxisSet2D' instance | print,AxisSet2D-method |
| print a 'AxisSet3D' instance | print,AxisSet3D-method |
| print a 'NamedAxis' | print,NamedAxis-method |
| Create an spherical random searchlight iterator | RandomSearchlight |
| readAFNIHeader | readAFNIHeader |
| Generic function to read a set of column vector from an input source (e.g. 'ColumnReader') | readColumns readColumns,ColumnReader,numeric-method |
| Generic function to read a sequence of elements from an input source | readElements readElements,BinaryReader,numeric-method |
| read header information of an image file | readHeader |
| Generic function to read image meta info given a file and a 'BrainFileDescriptor' instance. | readMetaInfo readMetaInfo,AFNIFileDescriptor-method readMetaInfo,NIfTIFileDescriptor-method |
| Create A Cuboid Region of Interest | RegionCube |
| Create a Spherical Region of Interest | RegionSphere |
| Create a square region of interest where the z-dimension is fixed at one voxel coordinate. | RegionSquare |
| Render an image to create a drawable image. | render render,BrainSlice,numeric,numeric,character-method |
| Render a slice at z coordinate | renderSlice |
| Generic function to remap the grid-to-world coordinates mapping of an image. | reorient reorient,BrainSpace,character-method |
| ROI | ROI-class |
| Create an instance of class 'ROIVector' | ROIVector |
| ROIVector | ROIVector-class |
| Create an instance of class 'ROIVolume' | ROIVolume |
| ROIVolume | ROIVolume-class |
| 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. | scaleSeries scaleSeries,BrainVector,logical,logical-method scaleSeries,BrainVector,logical,missing-method scaleSeries,BrainVector,missing,logical-method scaleSeries,BrainVector,missing,missing-method |
| Create an exhaustive searchlight iterator | Searchlight |
| Extract one or more series from object and return as ROI object | series series,BasisBrainVector,matrix-method series,BasisBrainVector,numeric-method series,BrainVector,LogicalBrainVolume-method series,BrainVector,matrix-method series,BrainVector,numeric-method series,BrainVector,ROIVolume-method series,SparseBrainVector,matrix-method series,SparseBrainVector,numeric-method series_roi series_roi,BrainVector,LogicalBrainVolume-method series_roi,BrainVector,matrix-method series_roi,BrainVector,numeric-method series_roi,BrainVector,ROIVolume-method |
| seriesIter | seriesIter seriesIter,BrainVector-method seriesIter,SparseBrainVector-method |
| show an 'AxisSet1D' | show,AxisSet1D-method |
| show an 'AxisSet2D' | show,AxisSet2D-method |
| show an 'AxisSet3D' | show,AxisSet3D-method |
| show an 'AxisSet4D' | show,AxisSet4D-method |
| show a 'BaseMetaInfo' | show,BaseMetaInfo-method |
| show a 'BrainSpace' | show,BrainSpace-method |
| show a 'BrainVector' | show,BrainVector-method |
| show a 'BrainVectorSource' | show,BrainVectorSource-method |
| show a 'BrainVolume' | show,BrainVolume-method |
| show a 'FileMetaInfo' | show,FileMetaInfo-method |
| show an 'NamedAxis' | show,NamedAxis-method |
| show a 'NullMetaInfo' | show,NullMetaInfo-method |
| show an 'ROIVolume' | show,ROIVolume-method |
| show a 'SparseBrainVector' | show,SparseBrainVector-method |
| Extract a 2D slice from an image volume | slice slice,BrainVolume,numeric,BrainSpace,AxisSet3D-method slice,BrainVolume,numeric,numeric,missing-method |
| sliceData | sliceData |
| Generic function to extract geometric properties of an image. | space space,BrainData-method space,BrainSpace-method space,IndexLookupVolume-method |
| Generic function to extract the voxel dimensions of an image | spacing spacing,BrainData-method spacing,BrainSpace-method |
| SparseBrainVector | SparseBrainVector SparseBrainVector-class |
| SparseBrainVectorSource | SparseBrainVectorSource SparseBrainVectorSource-class |
| SparseBrainVolume | SparseBrainVolume SparseBrainVolume-class |
| Generic function to fill disjoint sets of values with the output of a function | splitFill splitFill,BrainVolume,factor,function-method |
| Generic function to summarize subsets of an object by first splitting by row and then "reducing" by a summary 'function' | splitReduce splitReduce,BrainVector,factor,function-method splitReduce,BrainVector,factor,missing-method splitReduce,matrix,factor,function-method splitReduce,matrix,factor,missing-method splitReduce,matrix,integer,function-method splitReduce,matrix,integer,missing-method |
| Generic function to center/scale row-subsets of a matrix or matrix-like object | splitScale splitScale,DenseBrainVector,factor,logical,logical-method splitScale,DenseBrainVector,factor,logical,missing-method splitScale,DenseBrainVector,factor,missing,missing-method splitScale,matrix,factor,logical,logical-method splitScale,matrix,factor,missing,missing-method |
| Generic function to strip extension from file name, given a 'BrainFileDescriptor' instance. | stripExtension stripExtension,BrainFileDescriptor,character-method |
| Generic function to extract a sub-vector from a 'BrainVector' object. | subVector subVector,DenseBrainVector,numeric-method subVector,SparseBrainVector,numeric-method |
| Generic function to extract a one or more individual volumes from a four-dimensional image | takeVolume takeVolume,BrainVector,numeric-method takeVolume,SparseBrainVector,numeric-method |
| Generic getter to extract image coordinate transformation | trans trans,BrainData-method trans,BrainMetaInfo-method trans,BrainSpace-method trans,NIfTIMetaInfo-method |
| Generic function to extract data values of object | values values,ROIVector-method values,ROIVolume-method |
| extract voxel coordinates | voxels voxels,Kernel-method |
| Generic function to write a sequence of elements from an input source | writeElements writeElements,BinaryWriter,numeric-method |
| Generic function to write a 4D image vector to disk | writeVector writeVector,BrainVector,character,character,missing-method writeVector,BrainVector,character,missing,character,ANY-method writeVector,BrainVector,character,missing,character-method writeVector,BrainVector,character,missing,missing-method |
| Generic function to write a 3D image volume to disk | writeVolume writeVolume,BrainVolume,character,character,missing-method writeVolume,BrainVolume,character,missing,character-method writeVolume,BrainVolume,character,missing,missing-method writeVolume,ClusteredBrainVolume,character,missing,missing-method |
