This package is considered a duplicate. The official version of this package is found at:https://bbuchsbaum.r-universe.dev/neuroim2
Package: neuroim2 0.13.0
Bradley R Buchsbaum
neuroim2: Data Structures for Brain Imaging Data
A collection of data structures and methods for handling volumetric brain imaging data, with a focus on functional magnetic resonance imaging (fMRI). Provides efficient representations for three-dimensional and four-dimensional neuroimaging data through sparse and dense array implementations, memory-mapped file access for large datasets, and spatial transformation capabilities. Implements methods for image resampling, spatial filtering, region of interest analysis, and connected component labeling. General introduction to fMRI analysis can be found in Poldrack et al. (2024, "Handbook of functional MRI data analysis", <ISBN:9781108795760>).
Authors:
neuroim2_0.13.0.tar.gz
neuroim2_0.13.0.tar.gz(r-4.7-arm64)neuroim2_0.13.0.tar.gz(r-4.7-x86_64)neuroim2_0.13.0.tar.gz(r-4.6-arm64)neuroim2_0.13.0.tar.gz(r-4.6-x86_64)
neuroim2_0.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
neuroim2/json (API)
NEWS
| # Install 'neuroim2' in R: |
| install.packages('neuroim2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bbuchsbaum/neuroim2/issues
Pkgdown/docs site:https://bbuchsbaum.github.io
Last updated from:5916b19cc7. Checks:6 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 308 | ||
| linux-devel-x86_64 | OK | 305 | ||
| source / vignettes | OK | 325 | ||
| linux-release-arm64 | OK | 296 | ||
| linux-release-x86_64 | OK | 372 | ||
| wasm-release | OK | 185 |
Exports:add_dimaffine_to_axcodesaffine_to_orientationannotate_orientationANT_POSTappend_diagapply_affineapply_orientationArithas_canonicalas_mmapas_nifti_headeras.arrayas.denseas.listas.maskas.matrixas.sparseaxcodesaxcodes_to_orientationaxesBigNeuroVecbilateral_filterbilateral_filter_4dBinaryReaderBinaryWriterblobby_shapebootstrap_searchlightboundscentroidcentroidscgb_filtercgb_make_graphcgb_smoothcgb_smooth_loroclosecluster_searchlight_seriesclustered_searchlightClusteredNeuroVecClusteredNeuroVolColumnReaderCompareconcatconn_compconn_comp_3Dcoord_to_gridcoord_to_indexcoordscreateNIfTIHeadercube_shapecuboid_roidata_filedata_file_matchesdata_readerDenseNeuroVecDenseNeuroVoldeobliquedim_ofdot_reducedownsampledropdrop_dimecode_nameellipsoid_shapeembed_kernelextensionextensionsfile_matchesFileBackedNeuroVecfindAnatomy3Dfrom_matvecgaussian_blurget_afni_attributegrid_to_coordgrid_to_gridgrid_to_indexguided_filterhas_extensionsheaderheader_fileheader_file_matchesimageindex_to_coordindex_to_gridIndexLookupVolindicesINF_SUPinverse_transKernellabelslaplace_enhanceLEFT_RIGHTlinear_accesslist_afni_attributesload_dataLogicLogicalNeuroVollookupmake_time_weightsmap_valuesmapfMappedNeuroVecMappedNeuroVecSourcemapToColorsmaskmatricized_accessmatrixToQuaternmeanmeta_infoMetaInfondimNeuroHyperVecNeuroSliceNeuroSpaceNeuroVecNeuroVecSeqNeuroVolNeuroVolSourceNiftiExtensionNiftiExtensionCodesNIFTIMetaInfoNoneNullAxisnum_clustersobliquityorientation_inverse_affineorientation_to_axcodesorientation_transformOrientationList2DOrientationList3Doriginoutput_aligned_spaceparse_afni_extensionparse_extensionpartitionpatch_setperm_matplotplot_montageplot_orthoplot_overlayPOST_ANTprepare_confoundsquaternToMatrixrandom_searchlightread_columnsread_elementsread_headerread_hyper_vecread_imageread_meta_inforead_vecread_volread_vol_listreorientresampleresample_toresampled_searchlightrescale_affineresolve_cmapRIGHT_LEFTROICoordsROIVecROIVolscalescale_fill_neuroscale_seriessearchlightsearchlight_coordsseriesseries_roishowsimulate_fmrisliceslice_to_volume_affineslice2volumeslicesspacespacingSparseNeuroVecSparseNeuroVolspherical_roispherical_roi_setsplit_blockssplit_clusterssplit_fillsplit_reducesplit_scalesquare_roistrip_extensionsub_clusterssub_vectorsummarySummarySUP_INFtemporal_accesstheme_neuroTIMETimeAxisto_matvectransvaluesvec_from_volsvectorsvolsvolume_labelsvox2out_voxvoxel_sizesvoxelswhich_dimwrite_elementswrite_vecwrite_vol
Dependencies:assertthatbigassertrbigparallelrbigstatsrbitcachemclicodetoolscowplotcpp11dbscandeflistdigestdoParallelfarverfastmapffflockforeachfuturefuture.applygenericsggplot2globalsgluegtableisobanditeratorslabelinglatticelifecyclelistenvmagrittrMatrixmemoisemmapparallellypillarpkgconfigpspurrrR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRhpcBLASctlrlangrmioRNiftiRNiftyRegRSpectraS7scalesstringistringrtibbleutf8vctrsviridisLitewithr
Advanced 3D Volume Patterns
Rendered fromImageVolumes.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2025-04-10
Advanced NeuroVec Patterns
Rendered fromNeuroVector.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2025-04-10
Advanced ROI Construction
Rendered fromregionOfInterest.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2025-04-10
Advanced Split, Map, and Reduce
Rendered frompipelines.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2025-04-10
Choosing a Backend
Rendered fromChoosingBackends.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-04-16
ClusteredNeuroVec: Parcel-based 4D Analysis
Rendered fromclustered-neurovec.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-01-14
Coordinate Systems and Spatial Transforms
Rendered fromcoordinate-systems.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-04-16
neuroim2 Cookbook
Rendered fromCookbook.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-01-14
Overview: Getting Started with neuroim2
Rendered fromOverview.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-01-14
Resampling, downsampling, and reorientation
Rendered fromResampling.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-01-14
ROIs, Searchlights, and Pipelines
Rendered fromAnalysisWorkflows.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-04-16
Slice visualization with neuroim2
Rendered fromslice-visualization.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-04-16
Smoothing and filtering with neuroim2
Rendered fromSmoothing.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-01-14
Working with Volumes and Vectors
Rendered fromVolumesAndVectors.Rmdusingknitr::rmarkdownon Jun 15 2026.Last update: 2026-04-16
Started: 2026-04-16
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| neuroim2: neuroimaging data structures for analysis | neuroim2-package neuroim2 |
| [[ | [ [,AbstractSparseNeuroVec,numeric,numeric,ANY-method [,DenseNeuroVol,integer,missing,ANY-method [,DenseNeuroVol,numeric,missing,ANY-method [,DenseNeuroVol,ROIVol,missing,ANY-method [,NeuroVol,ROICoords,missing,ANY-method [,NeuroVol,ROIVol,missing,ANY-method [,ROICoords,numeric,missing,ANY-method [,ROIVol,logical,missing,ANY-method [,ROIVol,logical,numeric,ANY-method [,ROIVol,matrix,missing,ANY-method [,ROIVol,matrix,numeric,ANY-method [,ROIVol,missing,missing,ANY-method [,ROIVol,missing,numeric,ANY-method [,ROIVol,numeric,missing,ANY-method [,ROIVol,numeric,numeric,ANY-method [,ROIVol,ROICoords,missing,ANY-method [,ROIVol,ROICoords,numeric,ANY-method [,SparseNeuroVol,numeric,numeric,ANY-method [[,NeuroVec,character-method [[,NeuroVec,numeric-method |
| [[ | [[,AbstractSparseNeuroVec,numeric-method |
| Extract Element from NeuroVecSeq | [[,NeuroVecSeq,numeric-method |
| AbstractSparseNeuroVec Class | AbstractSparseNeuroVec-class |
| Add a Dimension to an Object | add_dim add_dim,NeuroSpace,numeric-method |
| Affine utility functions | affine_utils append_diag apply_affine dot_reduce from_matvec obliquity rescale_affine to_matvec voxel_sizes |
| Pre-defined anatomical axes | anatomical_axes ANT_POST INF_SUP LEFT_RIGHT POST_ANT RIGHT_LEFT SUP_INF |
| Add L/R and A/P/S/I annotations (optional) | annotate_orientation |
| Arithmetic Operations | Arith,ClusteredNeuroVol,ClusteredNeuroVol-method Arith,ClusteredNeuroVol,NeuroVol-method Arith,ClusteredNeuroVol,numeric-method Arith,DenseNeuroVec,DenseNeuroVec-method Arith,DenseNeuroVol,DenseNeuroVol-method Arith,DenseNeuroVol,numeric-method Arith,NeuroVec,NeuroVec-method Arith,NeuroVec,NeuroVol-method Arith,NeuroVol,ClusteredNeuroVol-method Arith,NeuroVol,NeuroVec-method Arith,NeuroVol,SparseNeuroVol-method Arith,numeric,ClusteredNeuroVol-method Arith,numeric,DenseNeuroVol-method Arith,numeric,SparseNeuroVol-method Arith,ROIVol,ROIVol-method Arith,SparseNeuroVec,SparseNeuroVec-method Arith,SparseNeuroVol,NeuroVol-method Arith,SparseNeuroVol,numeric-method Arith,SparseNeuroVol,SparseNeuroVol-method Arith-methods |
| ArrayLike3D Class | ArrayLike3D-class |
| ArrayLike4D Class | ArrayLike4D-class |
| ArrayLike5D Class | ArrayLike5D-class |
| Reorient Image to Canonical (RAS+) Orientation | as_canonical |
| Convert a NeuroVec to a memory-mapped representation | as_mmap as_mmap,FileBackedNeuroVec-method as_mmap,MappedNeuroVec-method as_mmap,NeuroVec-method as_mmap,SparseNeuroVec-method as_mmap-methods |
| Construct a Minimal NIfTI-1 Header from a NeuroVol | as_nifti_header |
| Convert ClusteredNeuroVol to DenseNeuroVol | as-ClusteredNeuroVol-DenseNeuroVol coerce,ClusteredNeuroVol,DenseNeuroVol-method |
| Generic as.array Method | as.array |
| Convert ClusteredNeuroVol to a base array | as.array,ClusteredNeuroVol-method as.array,SparseNeuroVec-method as.array,SparseNeuroVol-method |
| Convert to dense representation | as.dense |
| Convert a NeuroVecSeq to a DenseNeuroVec | as.dense,ClusteredNeuroVol-method as.dense,DenseNeuroVol-method as.dense,NeuroVecSeq-method as.dense,ROIVol-method as.dense,SparseNeuroVec-method as.dense,SparseNeuroVol-method |
| Convert FileBackedNeuroVec to List | as.list,FileBackedNeuroVec-method as.list,NeuroVec-method as.list,SparseNeuroVec-method |
| as.logical | as.logical as.logical,NeuroVol-method as.logical,ROIVol-method |
| Convert to a LogicalNeuroVol | as.mask |
| Convert NeuroVol to a mask | as.mask,NeuroVol,missing-method as.mask,NeuroVol,numeric-method |
| Generic as.matrix Method | as.matrix |
| convert a 'NeuroVec' to a matrix | as.matrix,AbstractSparseNeuroVec-method as.matrix,ClusteredNeuroVec-method as.matrix,DenseNeuroVec-method as.matrix,MappedNeuroVec-method as.matrix,NeuroVec-method as.matrix,NeuroVecSeq-method as.matrix,ROIVec-method |
| Convert SparseNeuroVol to numeric | as.numeric,ROIVol-method as.numeric,SparseNeuroVol-method |
| Generic Method for Converting Objects to Raster Format | as.raster |
| Convert to from dense to sparse representation | as.sparse |
| Convert DenseNeuroVec to sparse representation using mask | as.sparse,DenseNeuroVec,LogicalNeuroVol-method as.sparse,DenseNeuroVec,numeric-method as.sparse,DenseNeuroVol,LogicalNeuroVol-method as.sparse,DenseNeuroVol,numeric-method as.sparse,ROIVol,ANY-method |
| Convert SparseNeuroVol to a base vector | as.vector,SparseNeuroVol-method |
| Get Orientation Axis Codes | axcodes axcodes,matrix-method axcodes,NeuroObj-method axcodes,NeuroSpace-method |
| Extract Image Axes | axes axes,NeuroSpace-method |
| AxisSet | AxisSet-class |
| AxisSet1D | AxisSet1D-class |
| AxisSet2D | AxisSet2D-class |
| AxisSet3D Class | AxisSet3D-class |
| AxisSet4D Class | AxisSet4D-class |
| AxisSet5D Class | AxisSet5D-class |
| Create a Memory-Mapped Neuroimaging Vector | BigNeuroVec |
| BigNeuroVec Class | BigNeuroVec-class |
| Apply a bilateral filter to a volumetric image | bilateral_filter |
| Apply a 4D bilateral filter to a NeuroVec | bilateral_filter_4d |
| Create Binary Reader Object | BinaryReader |
| BinaryReader Class | BinaryReader-class |
| Create Binary Writer Object | BinaryWriter |
| BinaryWriter Class | BinaryWriter-class |
| Extract Spatial Bounds of an Image | bounds bounds,NeuroSpace-method |
| return the centroid of an object | centroid centroid,NeuroSpace-method centroid,ROICoords-method |
| Return a matrix of centroids of an object | centroids centroids,ClusteredNeuroVec-method centroids,ClusteredNeuroVol-method |
| Correlation-guided bilateral filtering (convenience wrapper) | cgb_filter |
| Build a correlation-guided bilateral (CGB) graph | cgb_make_graph |
| Apply a precomputed CGB graph to volumetric data | cgb_smooth |
| Leave-one-run-out smoothing helper | cgb_smooth_loro |
| Close a BinaryReader or BinaryWriter | close,BinaryReader-method close,BinaryWriter-method |
| Cluster-centroid searchlight over cluster time-series | cluster_searchlight_series |
| Create a clustered searchlight iterator | clustered_searchlight |
| ClusteredNeuroVec: Cluster-aware 4D neuroimaging data | ClusteredNeuroVec |
| ClusteredNeuroVec Class | ClusteredNeuroVec-class |
| ClusteredNeuroVol Class | ClusteredNeuroVol ClusteredNeuroVol-class |
| Create Column Reader Object | ColumnReader |
| ColumnReader | ColumnReader-class |
| Comparison Operations | Compare,DenseNeuroVol,DenseNeuroVol-method Compare,DenseNeuroVol,numeric-method Compare,NeuroVec,NeuroVec-method Compare,numeric,DenseNeuroVol-method Compare,numeric,SparseNeuroVol-method Compare,SparseNeuroVol,numeric-method Compare-methods |
| Concatenate two objects in the time dimension | concat concat,AbstractSparseNeuroVec,missing-method concat,DenseNeuroVol,DenseNeuroVol-method concat,DenseNeuroVol,missing-method concat,NeuroVec,NeuroVec-method concat,NeuroVec,NeuroVol-method concat,NeuroVol,NeuroVec-method concat,ROIVec,ROIVec-method concat,SparseNeuroVec,SparseNeuroVec-method |
| Connected components | conn_comp conn_comp,NeuroVol-method |
| Extract Connected Components from a 3D Binary Mask | conn_comp_3D |
| convert n-dimensional real world coordinates to grid coordinates | coord_to_grid coord_to_grid,NeuroSpace,matrix-method coord_to_grid,NeuroSpace,numeric-method coord_to_grid,NeuroVol,matrix-method coord_to_grid,NeuroVol,numeric-method |
| convert n-dimensional real world coordinates to 1D indices | coord_to_index coord_to_index,NeuroSpace,matrix-method coord_to_index,NeuroSpace,numeric-method coord_to_index,NeuroVol,matrix-method |
| Extract coordinates from an object | coords |
| Extract Coordinates from an IndexLookupVol Object | coords,AbstractSparseNeuroVec-method coords,IndexLookupVol-method coords,ROICoords-method coords,ROIVol-method |
| Create an Empty NIfTI-1 Header List | createNIfTIHeader |
| Create A Cuboid Region of Interest | cuboid_roi |
| Generic function to get the name of the data file, given a file name and a 'FileFormat' instance. | data_file data_file,FileFormat,character-method |
| Generic function to test whether a file name conforms to the given a 'FileFormat' instance. Will test for match to data file only | data_file_matches data_file_matches,FileFormat,character-method |
| Create a Data Reader | data_reader |
| Create Data Reader for AFNI Format | data_reader,AFNIMetaInfo-method data_reader,NIFTIMetaInfo-method |
| DenseNeuroVec Class | DenseNeuroVec DenseNeuroVec-class |
| DenseNeuroVol Class | DenseNeuroVol DenseNeuroVol-class |
| Deoblique a Neuroimaging Space or Volume | deoblique |
| Get the length of a given dimension of an object | dim_of dim_of,NeuroSpace,NamedAxis-method |
| Get Dimensions of FileMetaInfo Object | dim,ClusteredNeuroVec-method dim,FileMetaInfo-method dim,NeuroHyperVec-method dim,NeuroObj-method dim,NeuroSpace-method dim,ROICoords-method dim,ROIVol-method |
| Downsample an Image | downsample downsample,DenseNeuroVec-method downsample,DenseNeuroVol-method downsample,NeuroVec-method downsample,NeuroVol-method downsample,SparseNeuroVec-method |
| Generic Drop Method | drop |
| Drop a Dimension from an Object | drop_dim drop_dim,AxisSet2D,missing-method drop_dim,AxisSet2D,numeric-method drop_dim,AxisSet3D,missing-method drop_dim,AxisSet3D,numeric-method drop_dim,NeuroSpace,missing-method drop_dim,NeuroSpace,numeric-method |
| Drop a dimension | drop,NeuroVec-method |
| Get Extension Code Name | ecode_name |
| Generic function to position kernel in a position in image space | embed_kernel embed_kernel,Kernel,NeuroSpace,numeric-method |
| Get Extension by Code | extension extension,NiftiExtensionList,numeric-method |
| Get Extensions from an Object | extensions |
| Array-like access for 3-dimensional data structures | extractor3d [,ArrayLike3D,matrix,missing,ANY-method [,ArrayLike3D,missing,missing,ANY-method [,ArrayLike3D,missing,numeric,ANY-method [,ArrayLike3D,numeric,missing,ANY-method |
| Array-like access for 4-dimensional data structures | extractor4d [,ArrayLike4D,integer,missing,ANY-method [,ArrayLike4D,matrix,missing,ANY-method [,ArrayLike4D,missing,missing,ANY-method [,ArrayLike4D,missing,numeric,ANY-method [,ArrayLike4D,numeric,missing,ANY-method [,ArrayLike4D,numeric,numeric,ANY-method [,ClusteredNeuroVec,missing,missing,ANY-method [,ClusteredNeuroVec,numeric,numeric,ANY-method |
| 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 | file_matches file_matches,FileFormat,character-method |
| Create a File-Backed Neuroimaging Vector | FileBackedNeuroVec |
| FileBackedNeuroVec Class | FileBackedNeuroVec-class |
| FileFormat Class | FileFormat-class |
| File Format Operations for Neuroimaging Data | FileFormat-operations |
| FileMetaInfo Class | AFNIMetaInfo-class FileMetaInfo-class NIFTIMetaInfo-class |
| FileSource Class | FileSource-class |
| Find 3D anatomical orientation from axis abbreviations | findAnatomy3D |
| Gaussian Blur for Volumetric Images | gaussian_blur |
| Get AFNI Attribute from Extension | get_afni_attribute |
| Generic function to convert N-dimensional grid coordinates to real world coordinates | grid_to_coord grid_to_coord,NeuroSpace,matrix-method grid_to_coord,NeuroSpace,numeric-method grid_to_coord,NeuroVol,matrix-method |
| Generic function to convert voxel coordinates in the reference space (LPI) to native array space. | grid_to_grid grid_to_grid,matrix,matrix-method grid_to_grid,NeuroSpace,matrix-method |
| Generic function to convert N-dimensional grid coordinates to 1D indices | grid_to_index grid_to_index,NeuroSlice,matrix-method grid_to_index,NeuroSlice,numeric-method grid_to_index,NeuroSpace,matrix-method grid_to_index,NeuroSpace,numeric-method grid_to_index,NeuroVol,matrix-method grid_to_index,NeuroVol,numeric-method |
| Edge-Preserving Guided Filter for Volumetric Images | guided_filter |
| Check if Extensions are Present | has_extensions has_extensions,list-method has_extensions,NiftiExtensionList-method |
| Access NIfTI Header Information | header header,character-method header,FileMetaInfo-method |
| Generic function to get the name of the header file, given a file name and a 'FileFormat' instance. | header_file header_file,FileFormat,character-method |
| Generic function to test whether a file name conforms to the given 'FileFormat' instance. Will test for match to header file only | header_file_matches header_file_matches,FileFormat,character-method |
| Generic Image Method for Creating Visual Representations | image |
| convert 1d indices to n-dimensional real world coordinates | index_to_coord index_to_coord,NeuroSpace,integer-method index_to_coord,NeuroSpace,numeric-method index_to_coord,NeuroVec,integer-method index_to_coord,NeuroVol,integer-method |
| Convert 1d indices to n-dimensional grid coordinates | index_to_grid index_to_grid,NeuroSlice,numeric-method index_to_grid,NeuroSpace,numeric-method index_to_grid,NeuroVec,index-method index_to_grid,NeuroVec,integer-method index_to_grid,NeuroVol,index-method index_to_grid,NeuroVol,integer-method |
| IndexLookupVol Class | IndexLookupVol IndexLookupVol-class |
| Extract indices | indices |
| Get Indices from an IndexLookupVol Object | indices,AbstractSparseNeuroVec-method indices,IndexLookupVol-method indices,ROIVec-method indices,ROIVol-method |
| Extract inverse image coordinate transformation | inverse_trans inverse_trans,NeuroSpace-method |
| Create a Kernel object from a function of distance from kernel center | Kernel |
| Kernel | Kernel-class |
| Get Labels from ClusteredNeuroVec | labels,ClusteredNeuroVec-method |
| Laplacian Enhancement Filter for Volumetric Images | laplace_enhance |
| Get length of NeuroVec object | length,ClusteredNeuroVec-method length,NeuroVec-method length,NeuroVecSeq-method length,ROICoords-method length,ROIVol-method |
| Extract values from an array-like object using linear indexing. | linear_access |
| Linear Access Method for FileBackedNeuroVec | linear_access,AbstractSparseNeuroVec,numeric-method linear_access,DenseNeuroVec,integer-method linear_access,DenseNeuroVec,numeric-method linear_access,DenseNeuroVol,integer-method linear_access,DenseNeuroVol,numeric-method linear_access,FileBackedNeuroVec,numeric-method linear_access,MappedNeuroVec,numeric-method linear_access,NeuroHyperVec,ANY-method linear_access,NeuroVecSeq,numeric-method linear_access,SparseNeuroVol,numeric-method |
| List AFNI Attributes in Extension | list_afni_attributes |
| Load image data from a NeuroVecSource object | load_data,MappedNeuroVecSource-method load_data,NeuroVecSource-method load_data,NeuroVolSource-method load_data,SparseNeuroVecSource-method |
| Logic Operations for Neuroimaging Volumes | Logic,DenseNeuroVol,DenseNeuroVol-method Logic,logical,NeuroVol-method Logic,NeuroVol,logical-method Logic,NeuroVol,SparseNeuroVol-method Logic,SparseNeuroVol,NeuroVol-method Logic,SparseNeuroVol,SparseNeuroVol-method Logic-methods |
| LogicalNeuroVol Class | LogicalNeuroVol LogicalNeuroVol-class |
| Index Lookup operation | lookup |
| Lookup Values in an IndexLookupVol Object | lookup,AbstractSparseNeuroVec,numeric-method lookup,IndexLookupVol,numeric-method |
| Build smooth time weights from motion/outlier metrics | make_time_weights |
| Map Values from One Set to Another Using a User-supplied Lookup Table | map_values map_values,NeuroVol,list-method map_values,NeuroVol,matrix-method |
| Apply a function to an object. | mapf mapf,NeuroVol,Kernel-method |
| MappedNeuroVec Class | MappedNeuroVec MappedNeuroVec-class |
| MappedNeuroVecSource Class | MappedNeuroVecSource MappedNeuroVecSource-class |
| Map intensity values to colors | mapToColors |
| Extract Mask from Neuroimaging Object | mask mask,AbstractSparseNeuroVec-method mask,ClusteredNeuroVol-method mask,DenseNeuroVec-method mask,DenseNeuroVol-method mask,FileBackedNeuroVec-method mask,LogicalNeuroVol-method mask,MappedNeuroVec-method mask,NeuroHyperVec-method mask,NeuroSlice-method mask,SparseNeuroVecSource-method |
| Extract values from a 4D tensor using a matrix of time-space indices. | matricized_access matricized_access,BigNeuroVec,integer-method matricized_access,BigNeuroVec,matrix-method matricized_access,BigNeuroVec,numeric-method matricized_access,SparseNeuroVec,integer-method matricized_access,SparseNeuroVec,matrix-method matricized_access,SparseNeuroVec,numeric-method |
| Convert a Transformation Matrix to a Quaternion Representation | matrixToQuatern |
| Temporal Mean of a NeuroVec | mean,DenseNeuroVec-method mean,NeuroVec-method mean,SparseNeuroVec-method mean-methods |
| Lightweight metadata for neuroimaging files | meta_info meta_info,character-method meta_info,FileMetaInfo-method |
| Create Neuroimaging Metadata Object | MetaInfo |
| MetaInfo Class | MetaInfo-class |
| NamedAxis | NamedAxis-class |
| Extract the number of dimensions of an object | ndim ndim,AxisSet-method ndim,ClusteredNeuroVec-method ndim,NeuroHyperVec-method ndim,NeuroObj-method ndim,NeuroSpace-method |
| Downsampling Methods for Neuroimaging Objects | neuro-downsample |
| Arithmetic and Comparison Operations for Neuroimaging Objects | neuro-ops |
| Resampling Methods for Neuroimaging Objects | neuro-resample |
| NeuroBucket | NeuroBucket-class |
| Constructor for NeuroHyperVec class | NeuroHyperVec |
| NeuroHyperVec Class | NeuroHyperVec-class [,NeuroHyperVec,ANY,ANY,ANY-method [.NeuroHyperVec |
| NeuroObj Class | NeuroObj-class |
| NeuroSlice: 2D Neuroimaging Data Container | NeuroSlice |
| NeuroSlice Class | NeuroSlice-class |
| NeuroSpace: Spatial Reference System for Neuroimaging Data | NeuroSpace |
| NeuroSpace Class | NeuroSpace-class |
| NeuroVec Class | NeuroVec NeuroVec-class |
| NeuroVecSeq: A Container for Sequential NeuroVec Objects | NeuroVecSeq |
| NeuroVecSeq Class | NeuroVecSeq-class |
| NeuroVecSource | NeuroVecSource |
| NeuroVecSource Class | NeuroVecSource-class |
| NeuroVol: 3D Neuroimaging Volume Class | NeuroVol |
| NeuroVol Class | NeuroVol-class |
| Constructor for NeuroVolSource | NeuroVolSource |
| Create a NIfTI Extension | NiftiExtension |
| NiftiExtension Class | NiftiExtension-class show,NiftiExtension-method |
| Known NIfTI Extension Codes | NiftiExtensionCodes |
| NiftiExtensionList Class | NiftiExtensionList-class show,NiftiExtensionList-method |
| Create NIFTI Format Metadata Object | NIFTIMetaInfo |
| Pre-defined null axis | None |
| Logical Negation for Neuroimaging Volumes | !,DenseNeuroVol-method !,SparseNeuroVol-method not-methods |
| Pre-defined null axis set | NullAxis |
| Number of Clusters | num_clusters num_clusters,ClusteredNeuroVec-method num_clusters,ClusteredNeuroVol-method |
| numericOrMatrix Union | numericOrMatrix-class |
| Orientation utility functions | affine_to_axcodes affine_to_orientation apply_orientation axcodes_to_orientation orientation_inverse_affine orientation_to_axcodes orientation_transform orientation_utils |
| Pre-defined 2D orientation configurations | OrientationList2D |
| Pre-defined 3D orientation configurations | OrientationList3D |
| Extract Image Origin | origin origin,NeuroHyperVec-method origin,NeuroSpace-method origin,NeuroVec-method origin,NeuroVol-method |
| Parse AFNI Extension | parse_afni_extension |
| Parse NIfTI Extension Data | parse_extension |
| Partition an image into a set of disjoint clusters | partition partition,DenseNeuroVol,numeric-method partition,LogicalNeuroVol,integer-method partition,LogicalNeuroVol,numeric-method |
| Generate a set of coordinate "patches" of fixed size from an image object. | patch_set |
| Create a patch set from a NeuroVol object | patch_set,NeuroVol,numeric,LogicalNeuroVol-method patch_set,NeuroVol,numeric,missing-method |
| Extract permutation matrix associated with an image | perm_mat perm_mat,AxisSet2D-method perm_mat,AxisSet3D-method perm_mat,NeuroSpace-method |
| Plot a montage of axial (or any-plane) slices using facetting | plot_montage |
| Orthogonal three-plane view with optional crosshairs | plot_ortho |
| Composite an overlay map on a structural background | plot_overlay |
| Plot a NeuroSlice | plot,NeuroSlice,ANY-method plot,NeuroSlice-method plot,NeuroVol,missing-method plot,NeuroVol,NeuroVol-method plot,NeuroVol-method |
| Prepare weighted nuisance projectors for each run | prepare_confounds |
| Convert Quaternion Parameters to a Transformation Matrix | quaternToMatrix |
| Create a spherical random searchlight iterator | random_searchlight |
| read header information of an image file | read_header |
| Read a 5D image as a NeuroHyperVec | read_hyper_vec |
| read_image | read_image |
| Generic function to read image meta info given a file | read_meta_info read_meta_info,AFNIFormat-method read_meta_info,NIFTIFormat-method |
| read_vec | read_vec |
| Load a single 3D image volume from a file | read_vol |
| read_vol_list | read_vol_list |
| Remap the grid-to-world coordinates mapping of an image. | reorient reorient,NeuroSpace,character-method |
| Resample an Image to Match the Space of Another Image | resample resample,ClusteredNeuroVol,NeuroSpace-method resample,ClusteredNeuroVol,NeuroVol-method resample,NeuroVol,NeuroSpace-method resample,NeuroVol,NeuroVol-method |
| Resample an image with readable method names | resample_to |
| Create a resampled searchlight iterator | bootstrap_searchlight resampled_searchlight |
| Neuroimaging color palettes and helpers | resolve_cmap |
| ROI | ROI-class |
| Create ROI Coordinates Object | ROICoords |
| ROICoords | ROICoords-class |
| Create an instance of class 'ROIVec' | ROIVec |
| ROIVec | ROIVec-class |
| ROIVecWindow | ROIVecWindow-class |
| Create ROI Volume Object | ROIVol |
| ROIVol | ROIVol-class |
| ROIVolWindow | ROIVolWindow-class |
| Generic Scale Method | scale |
| A ggplot2 fill scale with neuroimaging-friendly defaults | scale_fill_neuro |
| 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. | scale_series scale_series,DenseNeuroVec,logical,logical-method scale_series,NeuroVec,logical,logical-method scale_series,NeuroVec,logical,missing-method scale_series,NeuroVec,missing,logical-method scale_series,NeuroVec,missing,missing-method scale_series,SparseNeuroVec,logical,logical-method |
| Create an exhaustive searchlight iterator | searchlight |
| Create an exhaustive searchlight iterator for voxel coordinates using spherical_roi | searchlight_coords |
| Convenience shape generators for 'resampled_searchlight()' | blobby_shape cube_shape ellipsoid_shape searchlight_shape_functions |
| Searchlight Analysis Methods | searchlight-methods |
| Extract one or more series from object | series series,AbstractSparseNeuroVec,integer-method series,AbstractSparseNeuroVec,matrix-method series,AbstractSparseNeuroVec,numeric-method series,AbstractSparseNeuroVec,ROICoords-method series,ClusteredNeuroVec,numeric-method series,DenseNeuroVec,integer-method series,DenseNeuroVec,matrix-method series,NeuroHyperVec,ANY-method series,NeuroVec,integer-method series,NeuroVec,LogicalNeuroVol-method series,NeuroVec,matrix-method series,NeuroVec,NeuroVol-method series,NeuroVec,numeric-method series,NeuroVec,ROICoords-method series,NeuroVecSeq,integer-method series,NeuroVecSeq,matrix-method series,NeuroVecSeq,numeric-method series_roi,NeuroVec,LogicalNeuroVol-method series_roi,NeuroVec,matrix-method series_roi,NeuroVec,numeric-method series_roi,NeuroVec,ROICoords-method series_roi,NeuroVecSeq,matrix-method |
| Extract time series from specific voxel coordinates and return as ROI object | series_roi |
| Show method for NamedAxis objects | show,AxisSet1D-method show,AxisSet2D-method show,AxisSet3D-method show,AxisSet4D-method show,ClusteredNeuroVec-method show,ClusteredNeuroVol-method show,DenseNeuroVec-method show,DenseNeuroVol-method show,FileMetaInfo-method show,IndexLookupVol-method show,Kernel-method show,MappedNeuroVec-method show,NamedAxis-method show,NeuroHyperVec-method show,NeuroSlice-method show,NeuroSpace-method show,NeuroVec-method show,NeuroVecSeq-method show,NeuroVecSource-method show,NeuroVol-method show,ROICoords-method show,ROIVec-method show,ROIVol-method show,SparseNeuroVec-method show,SparseNeuroVol-method |
| Simulate fMRI Data | simulate_fmri |
| Extract image slice | slice slice,NeuroVol,numeric,NeuroSpace,AxisSet3D-method slice,NeuroVol,numeric,numeric,missing-method |
| Extract an ordered series of 2D slices from a 3D or 4D object | slices slices,NeuroVol-method |
| Extract Geometric Properties of an Image | space space,ClusteredNeuroVec-method space,IndexLookupVol-method space,NeuroHyperVec-method space,NeuroObj-method space,NeuroSpace-method space,ROICoords-method |
| Space utility functions | output_aligned_space slice2volume slice_to_volume_affine space_utils vox2out_vox |
| Extract Voxel Dimensions of an Image | spacing spacing,NeuroHyperVec-method spacing,NeuroObj-method spacing,NeuroSpace-method spacing,ROICoords-method |
| SparseNeuroVec Class | SparseNeuroVec SparseNeuroVec-class |
| SparseNeuroVecSource Class | SparseNeuroVecSource-class |
| SparseNeuroVol Class | SparseNeuroVol SparseNeuroVol-class |
| Spatial Filtering Methods for Neuroimaging Data | spatial-filter |
| Create a Spherical Region of Interest | spherical_roi |
| Create Multiple Spherical Regions of Interest | spherical_roi_set |
| Cut a vector-valued object into a list of sub-blocks | split_blocks split_blocks,NeuroVec,factor-method split_blocks,NeuroVec,integer-method |
| Cut an object into a list of spatial or spatiotemporal clusters | split_clusters split_clusters,ClusteredNeuroVol,missing-method split_clusters,NeuroVec,ClusteredNeuroVol-method split_clusters,NeuroVec,integer-method split_clusters,NeuroVec,numeric-method split_clusters,NeuroVol,ClusteredNeuroVol-method split_clusters,NeuroVol,integer-method split_clusters,NeuroVol,numeric-method |
| Fill Disjoint Sets of Values with the Output of a Function | split_fill split_fill,NeuroVol,factor,function-method |
| Summarize Subsets of an Object by Splitting by Row and Applying a Summary Function | split_reduce split_reduce,matrix,factor,function-method split_reduce,matrix,factor,missing-method split_reduce,matrix,integer,function-method split_reduce,NeuroVec,factor,function-method split_reduce,NeuroVec,factor,missing-method |
| Center and/or Scale Row-subsets of a Matrix or Matrix-like Object | split_scale split_scale,DenseNeuroVec,factor,logical,logical-method split_scale,DenseNeuroVec,factor,logical,missing-method split_scale,DenseNeuroVec,factor,missing,missing-method split_scale,matrix,factor,logical,logical-method split_scale,matrix,factor,missing,missing-method |
| Create a square region of interest | square_roi |
| Generic function to strip extension from file name, given a 'FileFormat' instance. | strip_extension strip_extension,FileFormat,character-method |
| Select a Subset of Clusters | sub_clusters sub_clusters,ClusteredNeuroVec,character-method sub_clusters,ClusteredNeuroVec,integer-method sub_clusters,ClusteredNeuroVec,numeric-method sub_clusters,ClusteredNeuroVol,character-method sub_clusters,ClusteredNeuroVol,integer-method sub_clusters,ClusteredNeuroVol,numeric-method |
| Generic function to extract a sub-vector from a 'NeuroVec' object. | sub_vector sub_vector,AbstractSparseNeuroVec,numeric-method sub_vector,FileBackedNeuroVec,numeric-method sub_vector,NeuroVec,character-method sub_vector,NeuroVec,numeric-method sub_vector,NeuroVecSeq,numeric-method |
| Summary Methods for Neuroimaging Objects | Summary,DenseNeuroVol-method Summary,SparseNeuroVec-method Summary,SparseNeuroVol-method Summary-methods |
| Summary of Neuroimaging Objects | summary,DenseNeuroVec-method summary,NeuroVol-method summary,SparseNeuroVec-method summary-neuro-methods |
| Extract full sparse rows across time. | temporal_access temporal_access,BigNeuroVec,integer-method temporal_access,BigNeuroVec,numeric-method temporal_access,SparseNeuroVec,integer-method temporal_access,SparseNeuroVec,numeric-method |
| A minimal, publication-friendly theme for image slices | theme_neuro |
| Time axis | TIME |
| Time axis set | TimeAxis |
| Extract image coordinate transformation | trans trans,MetaInfo-method trans,NeuroHyperVec-method trans,NeuroObj-method trans,NeuroSpace-method trans,NIFTIMetaInfo-method |
| Extract Data Values of an Object | values values,ClusteredNeuroVec-method values,DenseNeuroVol-method values,ROIVec-method values,ROIVol-method values,SparseNeuroVol-method |
| Create NeuroVec from list of NeuroVol objects | vec_from_vols |
| Extract an ordered list of 1D vectors. | vectors vectors,DenseNeuroVec,missing-method vectors,matrix,integer-method vectors,matrix,missing-method vectors,matrix,numeric-method vectors,NeuroVec,logical-method vectors,NeuroVec,missing-method vectors,NeuroVec,numeric-method vectors,NeuroVecSeq,logical-method vectors,NeuroVecSeq,missing-method vectors,NeuroVecSeq,numeric-method vectors,ROIVec,integer-method vectors,ROIVec,logical-method vectors,ROIVec,missing-method vectors,ROIVec,numeric-method vectors,SparseNeuroVec,missing-method |
| Extract an ordered series of 3D volumes. | vols vols,NeuroVec,missing-method vols,NeuroVec,numeric-method |
| Get per-volume labels for a 'NeuroVec'. | volume_labels volume_labels,NeuroVec-method |
| extract voxel coordinates | voxels voxels,Kernel-method |
| Find Dimensions of a Given Axis | which_dim which_dim,NeuroSpace,NamedAxis-method |
| Write a sequence of elements from an input source | write_elements write_elements,BinaryWriter,numeric-method |
| Write a 4d image vector to disk | write_vec write_vec,NeuroHyperVec,character,character,missing-method write_vec,NeuroHyperVec,character,missing,character,ANY-method write_vec,NeuroHyperVec,character,missing,character-method write_vec,NeuroHyperVec,character,missing,missing-method write_vec,NeuroVec,character,character,missing-method write_vec,NeuroVec,character,missing,character,ANY-method write_vec,NeuroVec,character,missing,character-method write_vec,NeuroVec,character,missing,missing-method write_vec,ROIVec,character,missing,missing-method |
| Write a 3d image volume to disk | write_vol write_vol,ClusteredNeuroVol,character,missing,missing-method write_vol,NeuroVol,character,character,missing-method write_vol,NeuroVol,character,missing,character-method write_vol,NeuroVol,character,missing,missing-method write_vol,ROIVol,character,character,missing-method |
