{ "_id": "6a21f35acd65a98ecbd425ae", "Package": "neuroim2", "Type": "Package", "Title": "Data Structures for Brain Imaging Data", "Version": "0.16.0", "Author": "Bradley R Buchsbaum [aut, cre, cph]", "Authors@R": "c(\nperson(c(\"Bradley\", \"R\"), \"Buchsbaum\", role = c(\"aut\", \"cre\", \"cph\"), email = \"brad.buchsbaum@gmail.com\"))", "Maintainer": "Bradley R Buchsbaum ", "Description": "A collection of data structures and methods for handling\nvolumetric brain imaging data, with a focus on functional\nmagnetic resonance imaging (fMRI). Provides efficient\nrepresentations for three-dimensional and four-dimensional\nneuroimaging data through sparse and dense array\nimplementations, memory-mapped file access for large datasets,\nand spatial transformation capabilities. Implements methods for\nimage resampling, spatial filtering, region of interest\nanalysis, and connected component labeling. General\nintroduction to fMRI analysis can be found in Poldrack et al.\n(2024, \"Handbook of functional MRI data analysis\",\n).", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr, rmarkdown", "Collate": "'RcppExports.R' 'all_generic.R' 'all_class.R'\n'SparseNeuroVec-validity.R' 'affine_utils.R' 'afni_io.R'\n'array_like.R' 'axis.R' 'big_neurovec.R' 'binary_io.R' 'cgb.R'\n'cgb_nuisance.R' 'clustered_neurovec.R' 'clustervol.R'\n'common.R' 'conncomp.R' 'deoblique.R' 'downsample.R'\n'file_format.R' 'filebacked_neurovec.R' 'globals.R'\n'header_api.R' 'index_vol.R' 'mapped_neurovec.R' 'meta_info.R'\n'meta_info_api.R' 'neuro_obj.R' 'neurohypervec.R' 'neuroim.R'\n'neuroslice.R' 'neurospace.R' 'neurovec.R' 'neurovecseq.R'\n'neurovol.R' 'nifti_extensions.R' 'nifti_io.R' 'niml_io.R'\n'ops.R' 'orientation.R' 'palettes.R' 'plot-checkerboard.R'\n'plot-edge-overlay.R' 'plot-helpers.R' 'plot-montage.R'\n'plot-ortho.R' 'plot-overlay.R' 'read_image.R' 'resample.R'\n'resample_to.R' 'roi.R' 'searchlight.R' 'show_helpers.R'\n'simulate.R' 'space_utils.R' 'sparse_neurovec.R'\n'spat_filter.R' 'summary_methods.R' 'theme.R' 'zzz.R'", "RoxygenNote": "7.3.3", "URL": "https://github.com/bbuchsbaum/neuroim2,\nhttps://bbuchsbaum.github.io/neuroim2/", "BugReports": "https://github.com/bbuchsbaum/neuroim2/issues", "Language": "en-US", "Config/Needs/website": "bbuchsbaum/albersdown, albersdown", "Config/pak/sysreqs": "make libicu-dev", "Repository": "https://bbuchsbaum.r-universe.dev", "Date/Publication": "2026-06-04 20:10:05 UTC", "RemoteUrl": "https://github.com/bbuchsbaum/neuroim2", "RemoteRef": "HEAD", "RemoteSha": "234a1b985f4da8bb1433f719a685447a85ff23b2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-04 21:40:51 UTC", "User": "root" }, "MD5sum": "133296987ec5da0a183ece5d4b2efb08", "_user": "bbuchsbaum", "_type": "src", "_file": "neuroim2_0.16.0.tar.gz", "_fileid": "995f453c337a727fc8a63d30a94e3e59003d56bf1bff6de13d9f2eb2f04b5ac4", "_filesize": 1897703, "_sha256": "995f453c337a727fc8a63d30a94e3e59003d56bf1bff6de13d9f2eb2f04b5ac4", "_created": "2026-06-04T21:40:51.000Z", "_published": "2026-06-04T21:51:22.839Z", "_distro": "noble", "_jobs": [ { "job": 79621051754, "time": 348, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7423804840" }, { "job": 79621051775, "time": 382, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7423814234" }, { "job": 79621051797, "time": 344, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7423803453" }, { "job": 79621051793, "time": 337, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7423800195" }, { "job": 79621051654, "time": 239, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7423770372" }, { "job": 79621051636, "time": 443, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7423832848" }, { "job": 79621051702, "time": 226, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7423766139" }, { "job": 79621051682, "time": 540, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7423861839" }, { "job": 79620164373, "time": 333, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7423695455" }, { "job": 79621051621, "time": 164, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7423747026" }, { "job": 79621051712, "time": 352, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7423805087" }, { "job": 79621051767, "time": 433, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7423830364" }, { "job": 79621051774, "time": 406, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7423822006" } ], "_buildurl": "https://github.com/r-universe/bbuchsbaum/actions/runs/26981062125", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bbuchsbaum/neuroim2", "_commit": { "id": "234a1b985f4da8bb1433f719a685447a85ff23b2", "author": "bbuchsbaum ", "committer": "bbuchsbaum ", "message": "Insulate gaussian_blur to the mask (fix #22)\n\nThe masked path of gaussian_blur() used the mask only to select which\noutput voxels to write, not to insulate the convolution. Each in-mask\noutput read the full window of neighbor values (regardless of mask\nmembership) and normalized by the full kernel weight. Consequences:\n\n 1. Out-of-mask NaN/Inf (e.g. brain-exterior values in first-level\n statistic maps) propagated into in-mask outputs, silently erasing\n a ~window-voxel shell of the masked region.\n 2. Finite exterior values (e.g. zero padding) biased in-mask edge\n voxels, with no in-mask renormalization.\n\nRewrite gaussian_blur_cpp_impl to a renormalized smooth-in-mask\nconvolution (cf. AFNI 3dBlurInMask): out-of-mask and out-of-bounds\nneighbors are skipped entirely (their values are never read) and the\nkernel is renormalized by the in-mask weight sum. The center voxel is\nalways in-mask, so the denominator is always positive.\n\nAdd a normalize argument (default TRUE = corrected behavior) to\ngaussian_blur() and gaussian_blur_cpp; normalize = FALSE restores the\nexact legacy full-kernel behavior for back-compat.\n\nVerified: the new default matches the issue's smooth-in-mask workaround\nexactly on shared support; normalize = FALSE reproduces legacy output\nbit-for-bit. Adds regression tests covering NaN insulation, edge\nrenormalization, workaround equivalence, and legacy preservation.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) \n", "time": 1780603805 }, "_maintainer": { "name": "Bradley R Buchsbaum", "email": "brad.buchsbaum@gmail.com", "login": "bbuchsbaum", "description": "", "uuid": 53819 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "Matrix", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "purrr", "role": "Imports" }, { "package": "mmap", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "RcppParallel", "role": "Imports" }, { "package": "RNifti", "role": "Imports" }, { "package": "dbscan", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": 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"topics": [ "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" ] }, { "page": "as.numeric-methods", "title": "Convert SparseNeuroVol to numeric", "topics": [ "as.numeric,ROIVol-method", "as.numeric,SparseNeuroVol-method" ] }, { "page": "as.raster", "title": "Generic Method for Converting Objects to Raster Format", "topics": [ "as.raster" ] }, { "page": "as.sparse", "title": "Convert to from dense to sparse representation", "topics": [ "as.sparse" ] }, { "page": "as.sparse-methods", "title": "Convert DenseNeuroVec to sparse representation using mask", "topics": [ "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" ] }, { "page": "as.vector-methods", "title": "Convert SparseNeuroVol to a base vector", "topics": [ "as.vector,SparseNeuroVol-method" ] }, { "page": "automask-methods", "title": "Compute a brain-like mask from image intensities", "topics": [ "automask", "automask,AbstractSparseNeuroVec-method", "automask,DenseNeuroVec-method", "automask,FileBackedNeuroVec-method", "automask,MappedNeuroVec-method", "automask,NeuroVol-method" ] }, { "page": "axcodes-methods", "title": "Get Orientation Axis Codes", "topics": [ "axcodes", "axcodes,matrix-method", "axcodes,NeuroObj-method", "axcodes,NeuroSpace-method" ] }, { "page": "axes-methods", "title": "Extract Image Axes", "topics": [ "axes", "axes,NeuroSpace-method" ] }, { "page": "AxisSet-class", "title": "AxisSet", "topics": [ "AxisSet-class" ] }, { "page": "AxisSet1D-class", "title": "AxisSet1D", "topics": [ "AxisSet1D-class" ] }, { "page": "AxisSet2D-class", "title": "AxisSet2D", "topics": [ "AxisSet2D-class" ] }, { "page": "AxisSet3D-class", "title": "AxisSet3D Class", "topics": [ "AxisSet3D-class" ] }, { "page": "AxisSet4D-class", "title": "AxisSet4D Class", "topics": [ "AxisSet4D-class" ] }, { "page": "AxisSet5D-class", "title": "AxisSet5D Class", "topics": [ "AxisSet5D-class" ] }, { "page": "BigNeuroVec-methods", "title": "Create a Memory-Mapped Neuroimaging Vector", "topics": [ "BigNeuroVec" ] }, { "page": "BigNeuroVec-class", "title": "BigNeuroVec Class", "topics": [ "BigNeuroVec-class" ] }, { "page": "bilateral_filter", "title": "Apply a bilateral filter to a volumetric image", "topics": [ "bilateral_filter" ] }, { "page": "bilateral_filter_4d", "title": "Apply a 4D bilateral filter to a NeuroVec", "topics": [ "bilateral_filter_4d" ] }, { "page": "BinaryReader", "title": "Create Binary Reader Object", "topics": [ "BinaryReader" ] }, { "page": "BinaryReader-class", "title": "BinaryReader Class", "topics": [ "BinaryReader-class" ] }, { "page": "BinaryWriter", "title": "Create Binary Writer Object", "topics": [ "BinaryWriter" ] }, { "page": "BinaryWriter-class", "title": "BinaryWriter Class", "topics": [ "BinaryWriter-class" ] }, { "page": "bounds-methods", "title": "Extract Spatial Bounds of an Image", "topics": [ "bounds", "bounds,NeuroSpace-method" ] }, { "page": "centroid-methods", "title": "return the centroid of an object", "topics": [ "centroid", "centroid,NeuroSpace-method", "centroid,ROICoords-method" ] }, { "page": "centroids-methods", "title": "Return a matrix of centroids of an object", "topics": [ "centroids", "centroids,ClusteredNeuroVec-method", "centroids,ClusteredNeuroVol-method" ] }, { "page": "cgb_filter", "title": "Correlation-guided bilateral filtering (convenience wrapper)", "topics": [ "cgb_filter" ] }, { "page": "cgb_make_graph", "title": "Build a correlation-guided bilateral (CGB) graph", "topics": [ "cgb_make_graph" ] }, { "page": "cgb_smooth", "title": "Apply a precomputed CGB graph to volumetric data", "topics": [ "cgb_smooth" ] }, { "page": "cgb_smooth_loro", "title": "Leave-one-run-out smoothing helper", "topics": [ "cgb_smooth_loro" ] }, { "page": "clip_level-methods", "title": "Estimate an image clip level", "topics": [ "clip_level", "clip_level,AbstractSparseNeuroVec-method", "clip_level,DenseNeuroVec-method", "clip_level,FileBackedNeuroVec-method", "clip_level,MappedNeuroVec-method", "clip_level,NeuroVol-method" ] }, { "page": "close-methods", "title": "Close a BinaryReader or BinaryWriter", "topics": [ "close,BinaryReader-method", "close,BinaryWriter-method" ] }, { "page": "cluster_searchlight_series", "title": "Cluster-centroid searchlight over cluster time-series", "topics": [ "cluster_searchlight_series" ] }, { "page": "clustered_searchlight", "title": "Create a clustered searchlight iterator", "topics": [ "clustered_searchlight" ] }, { "page": "ClusteredNeuroVec", "title": "ClusteredNeuroVec: Cluster-aware 4D neuroimaging data", "topics": [ "ClusteredNeuroVec" ] }, { "page": "ClusteredNeuroVec-class", "title": "ClusteredNeuroVec Class", "topics": [ "ClusteredNeuroVec-class" ] }, { "page": "ClusteredNeuroVol-class", "title": "ClusteredNeuroVol Class", "topics": [ "ClusteredNeuroVol", "ClusteredNeuroVol-class" ] }, { "page": "ColumnReader", "title": "Create Column Reader Object", "topics": [ "ColumnReader" ] }, { "page": "ColumnReader-class", "title": "ColumnReader", "topics": [ "ColumnReader-class" ] }, { "page": "Compare-methods", "title": "Comparison Operations", "topics": [ "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" ] }, { "page": "concat-methods", "title": "Concatenate two objects in the time dimension", "topics": [ "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" ] }, { "page": "conn_comp-methods", "title": "Connected components", "topics": [ "conn_comp", "conn_comp,NeuroVol-method" ] }, { "page": "conn_comp_3D", "title": "Extract Connected Components from a 3D Binary Mask", "topics": [ "conn_comp_3D" ] }, { "page": "coord_to_grid-methods", "title": "convert n-dimensional real world coordinates to grid coordinates", "topics": [ "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" ] }, { "page": "coord_to_index-methods", "title": "convert n-dimensional real world coordinates to 1D indices", "topics": [ "coord_to_index", "coord_to_index,NeuroSpace,matrix-method", "coord_to_index,NeuroSpace,numeric-method", "coord_to_index,NeuroVol,matrix-method" ] }, { "page": "coords", "title": "Extract coordinates from an object", "topics": [ "coords" ] }, { "page": "coords-methods", "title": "Extract Coordinates from an IndexLookupVol Object", "topics": [ "coords,AbstractSparseNeuroVec-method", "coords,IndexLookupVol-method", "coords,ROICoords-method", "coords,ROIVol-method" ] }, { "page": "createNIfTIHeader", "title": "Create an Empty NIfTI-1 Header List", "topics": [ "createNIfTIHeader" ] }, { "page": "cuboid_roi", "title": "Create A Cuboid Region of Interest", "topics": [ "cuboid_roi" ] }, { "page": "data_file-methods", "title": "Generic function to get the name of the data file, given a file name and a 'FileFormat' instance.", "topics": [ "data_file", "data_file,FileFormat,character-method" ] }, { "page": "data_file_matches-methods", "title": "Generic function to test whether a file name conforms to the given a 'FileFormat' instance. Will test for match to data file only", "topics": [ "data_file_matches", "data_file_matches,FileFormat,character-method" ] }, { "page": "data_reader", "title": "Create a Data Reader", "topics": [ "data_reader" ] }, { "page": "data_reader-methods", "title": "Create Data Reader for AFNI Format", "topics": [ "data_reader,AFNIMetaInfo-method", "data_reader,NIFTIMetaInfo-method" ] }, { "page": "DenseNeuroVec-class", "title": "DenseNeuroVec Class", "topics": [ "DenseNeuroVec", "DenseNeuroVec-class" ] }, { "page": "DenseNeuroVol-class", "title": "DenseNeuroVol Class", "topics": [ "DenseNeuroVol", "DenseNeuroVol-class" ] }, { "page": "deoblique", "title": "Deoblique a Neuroimaging Space or Volume", "topics": [ "deoblique" ] }, { "page": "dim_of-methods", "title": "Get the length of a given dimension of an object", "topics": [ "dim_of", "dim_of,NeuroSpace,NamedAxis-method" ] }, { "page": "dim-methods", "title": "Get Dimensions of FileMetaInfo Object", "topics": [ "dim,ClusteredNeuroVec-method", "dim,FileMetaInfo-method", "dim,NeuroHyperVec-method", "dim,NeuroObj-method", "dim,NeuroSpace-method", "dim,ROICoords-method", "dim,ROIVol-method" ] }, { "page": "downsample-methods", "title": "Downsample an Image", "topics": [ "downsample", "downsample,DenseNeuroVec-method", "downsample,DenseNeuroVol-method", "downsample,NeuroVec-method", "downsample,NeuroVol-method", "downsample,SparseNeuroVec-method" ] }, { "page": "drop", "title": "Generic Drop Method", "topics": [ "drop" ] }, { "page": "drop_dim-methods", "title": "Drop a Dimension from an Object", "topics": [ "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" ] }, { "page": "drop-methods", "title": "Drop a dimension", "topics": [ "drop,NeuroVec-method" ] }, { "page": "ecode_name", "title": "Get Extension Code Name", "topics": [ "ecode_name" ] }, { "page": "embed_kernel-methods", "title": "Generic function to position kernel in a position in image space", "topics": [ "embed_kernel", "embed_kernel,Kernel,NeuroSpace,numeric-method" ] }, { "page": "enhance_stat_map", "title": "Enhance an unsmoothed statistical map for visualization", "topics": [ "enhance_stat_map" ] }, { "page": "extension", "title": "Get Extension by Code", "topics": [ "extension", "extension,NiftiExtensionList,numeric-method" ] }, { "page": "extensions", "title": "Get Extensions from an Object", "topics": [ "extensions" ] }, { "page": "extractor3d", "title": "Array-like access for 3-dimensional data structures", "topics": [ "extractor3d", "[,ArrayLike3D,matrix,missing,ANY-method", "[,ArrayLike3D,missing,missing,ANY-method", "[,ArrayLike3D,missing,numeric,ANY-method", "[,ArrayLike3D,numeric,missing,ANY-method" ] }, { "page": "extractor4d", "title": "Array-like access for 4-dimensional data structures", "topics": [ "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" ] }, { "page": "file_matches-methods", "title": "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", "topics": [ "file_matches", "file_matches,FileFormat,character-method" ] }, { "page": "FileBackedNeuroVec", "title": "Create a File-Backed Neuroimaging Vector", "topics": [ "FileBackedNeuroVec" ] }, { "page": "FileBackedNeuroVec-class", "title": "FileBackedNeuroVec Class", "topics": [ "FileBackedNeuroVec-class" ] }, { "page": "FileFormat-class", "title": "FileFormat Class", "topics": [ "FileFormat-class" ] }, { "page": "FileFormat-operations", "title": "File Format Operations for Neuroimaging Data", "topics": [ "FileFormat-operations" ] }, { "page": "FileMetaInfo-class", "title": "FileMetaInfo Class", "topics": [ "AFNIMetaInfo-class", "FileMetaInfo-class", "NIFTIMetaInfo-class" ] }, { "page": "FileSource-class", "title": "FileSource Class", "topics": [ "FileSource-class" ] }, { "page": "findAnatomy3D", "title": "Find 3D anatomical orientation from axis abbreviations", "topics": [ "findAnatomy3D" ] }, { "page": "gaussian_blur", "title": "Gaussian Blur for Volumetric Images", "topics": [ "gaussian_blur" ] }, { "page": "get_afni_attribute", "title": "Get AFNI Attribute from Extension", "topics": [ "get_afni_attribute" ] }, { "page": "grid_to_coord-methods", "title": "Generic function to convert N-dimensional grid coordinates to real world coordinates", "topics": [ "grid_to_coord", "grid_to_coord,NeuroSpace,matrix-method", "grid_to_coord,NeuroSpace,numeric-method", "grid_to_coord,NeuroVol,matrix-method" ] }, { "page": "grid_to_grid-methods", "title": "Generic function to convert voxel coordinates in the reference space (LPI) to native array space.", "topics": [ "grid_to_grid", "grid_to_grid,matrix,matrix-method", "grid_to_grid,NeuroSpace,matrix-method" ] }, { "page": "grid_to_index-methods", "title": "Generic function to convert N-dimensional grid coordinates to 1D indices", "topics": [ "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" ] }, { "page": "guided_filter", "title": "Edge-Preserving Guided Filter for Volumetric Images", "topics": [ "guided_filter" ] }, { "page": "has_extensions", "title": "Check if Extensions are Present", "topics": [ "has_extensions", "has_extensions,list-method", "has_extensions,NiftiExtensionList-method" ] }, { "page": "header-methods", "title": "Access NIfTI Header Information", "topics": [ "header", "header,character-method", "header,FileMetaInfo-method" ] }, { "page": "header_file-methods", "title": "Generic function to get the name of the header file, given a file name and a 'FileFormat' instance.", "topics": [ "header_file", "header_file,FileFormat,character-method" ] }, { "page": "header_file_matches-methods", "title": "Generic function to test whether a file name conforms to the given 'FileFormat' instance. Will test for match to header file only", "topics": [ "header_file_matches", "header_file_matches,FileFormat,character-method" ] }, { "page": "image", "title": "Generic Image Method for Creating Visual Representations", "topics": [ "image" ] }, { "page": "index_to_coord-methods", "title": "convert 1d indices to n-dimensional real world coordinates", "topics": [ "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" ] }, { "page": "index_to_grid-methods", "title": "Convert 1d indices to n-dimensional grid coordinates", "topics": [ "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" ] }, { "page": "IndexLookupVol-class", "title": "IndexLookupVol Class", "topics": [ "IndexLookupVol", "IndexLookupVol-class" ] }, { "page": "indices", "title": "Extract indices", "topics": [ "indices" ] }, { "page": "indices-methods", "title": "Get Indices from an IndexLookupVol Object", "topics": [ "indices,AbstractSparseNeuroVec-method", "indices,IndexLookupVol-method", "indices,ROIVec-method", "indices,ROIVol-method" ] }, { "page": "inverse_trans-methods", "title": "Extract inverse image coordinate transformation", "topics": [ "inverse_trans", "inverse_trans,NeuroSpace-method" ] }, { "page": "Kernel", "title": "Create a Kernel object from a function of distance from kernel center", "topics": [ "Kernel" ] }, { "page": "Kernel-class", "title": "Kernel", "topics": [ "Kernel-class" ] }, { "page": "labels-methods", "title": "Get Labels from ClusteredNeuroVec", "topics": [ "labels,ClusteredNeuroVec-method" ] }, { "page": "laplace_enhance", "title": "Laplacian Enhancement Filter for Volumetric Images", "topics": [ "laplace_enhance" ] }, { "page": "length-methods", "title": "Get length of NeuroVec object", "topics": [ "length,ClusteredNeuroVec-method", "length,NeuroVec-method", "length,NeuroVecSeq-method", "length,ROICoords-method", "length,ROIVol-method" ] }, { "page": "linear_access", "title": "Extract values from an array-like object using linear indexing.", "topics": [ "linear_access" ] }, { "page": "linear_access-methods", "title": "Linear Access Method for FileBackedNeuroVec", "topics": [ "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" ] }, { "page": "list_afni_attributes", "title": "List AFNI Attributes in Extension", "topics": [ "list_afni_attributes" ] }, { "page": "load_data-methods", "title": "Load image data from a NeuroVecSource object", "topics": [ "load_data,MappedNeuroVecSource-method", "load_data,NeuroVecSource-method", "load_data,NeuroVolSource-method", "load_data,SparseNeuroVecSource-method" ] }, { "page": "Logic-methods", "title": "Logic Operations for Neuroimaging Volumes", "topics": [ "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" ] }, { "page": "LogicalNeuroVol-class", "title": "LogicalNeuroVol Class", "topics": [ "LogicalNeuroVol", "LogicalNeuroVol-class" ] }, { "page": "lookup", "title": "Index Lookup operation", "topics": [ "lookup" ] }, { "page": "lookup-methods", "title": "Lookup Values in an IndexLookupVol Object", "topics": [ "lookup,AbstractSparseNeuroVec,numeric-method", "lookup,IndexLookupVol,numeric-method" ] }, { "page": "make_time_weights", "title": "Build smooth time weights from motion/outlier metrics", "topics": [ "make_time_weights" ] }, { "page": "map_values-methods", "title": "Map Values from One Set to Another Using a User-supplied Lookup Table", "topics": [ "map_values", "map_values,NeuroVol,list-method", "map_values,NeuroVol,matrix-method" ] }, { "page": "map-methods", "title": "Apply a function to an object.", "topics": [ "mapf", "mapf,NeuroVol,Kernel-method" ] }, { "page": "MappedNeuroVec-class", "title": "MappedNeuroVec Class", "topics": [ "MappedNeuroVec", "MappedNeuroVec-class" ] }, { "page": "MappedNeuroVecSource-class", "title": "MappedNeuroVecSource Class", "topics": [ "MappedNeuroVecSource", "MappedNeuroVecSource-class" ] }, { "page": "mapToColors", "title": "Map intensity values to colors", "topics": [ "mapToColors" ] }, { "page": "mask-methods", "title": "Extract Mask from Neuroimaging Object", "topics": [ "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" ] }, { "page": "matricized_access-methods", "title": "Extract values from a 4D tensor using a matrix of time-space indices.", "topics": [ "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" ] }, { "page": "matrixToQuatern", "title": "Convert a Transformation Matrix to a Quaternion Representation", "topics": [ "matrixToQuatern" ] }, { "page": "mean-methods", "title": "Temporal Mean of a NeuroVec", "topics": [ "mean,DenseNeuroVec-method", "mean,NeuroVec-method", "mean,SparseNeuroVec-method", "mean-methods" ] }, { "page": "meta_info", "title": "Lightweight metadata for neuroimaging files", "topics": [ "meta_info", "meta_info,character-method", "meta_info,FileMetaInfo-method" ] }, { "page": "MetaInfo", "title": "Create Neuroimaging Metadata Object", "topics": [ "MetaInfo" ] }, { "page": "MetaInfo-class", "title": "MetaInfo Class", "topics": [ "MetaInfo-class" ] }, { "page": "NamedAxis-class", "title": "NamedAxis", "topics": [ "NamedAxis-class" ] }, { "page": "ndim-methods", "title": "Extract the number of dimensions of an object", "topics": [ "ndim", "ndim,AxisSet-method", "ndim,ClusteredNeuroVec-method", "ndim,NeuroHyperVec-method", "ndim,NeuroObj-method", "ndim,NeuroSpace-method" ] }, { "page": "neuro-downsample", "title": "Downsampling Methods for Neuroimaging Objects", "topics": [ "neuro-downsample" ] }, { "page": "neuro-ops", "title": "Arithmetic and Comparison Operations for Neuroimaging Objects", "topics": [ "neuro-ops" ] }, { "page": "neuro-resample", "title": "Resampling Methods for Neuroimaging Objects", "topics": [ "neuro-resample" ] }, { "page": "NeuroBucket-class", "title": "NeuroBucket", "topics": [ "NeuroBucket-class" ] }, { "page": "NeuroHyperVec", "title": "Constructor for NeuroHyperVec class", "topics": [ "NeuroHyperVec" ] }, { "page": "NeuroHyperVec-class", "title": "NeuroHyperVec Class", "topics": [ "NeuroHyperVec-class", "[,NeuroHyperVec,ANY,ANY,ANY-method", "[.NeuroHyperVec" ] }, { "page": "NeuroObj-class", "title": "NeuroObj Class", "topics": [ "NeuroObj-class" ] }, { "page": "NeuroSlice", "title": "NeuroSlice: 2D Neuroimaging Data Container", "topics": [ "NeuroSlice" ] }, { "page": "NeuroSlice-class", "title": "NeuroSlice Class", "topics": [ "NeuroSlice-class" ] }, { "page": "NeuroSpace", "title": "NeuroSpace: Spatial Reference System for Neuroimaging Data", "topics": [ "NeuroSpace" ] }, { "page": "NeuroSpace-class", "title": "NeuroSpace Class", "topics": [ "NeuroSpace-class" ] }, { "page": "NeuroVec-class", "title": "NeuroVec Class", "topics": [ "NeuroVec", "NeuroVec-class" ] }, { "page": "NeuroVecSeq", "title": "NeuroVecSeq: A Container for Sequential NeuroVec Objects", "topics": [ "NeuroVecSeq" ] }, { "page": "NeuroVecSeq-class", "title": "NeuroVecSeq Class", "topics": [ "NeuroVecSeq-class" ] }, { "page": "NeuroVecSource", "title": "NeuroVecSource", "topics": [ "NeuroVecSource" ] }, { "page": "NeuroVecSource-class", "title": "NeuroVecSource Class", "topics": [ "NeuroVecSource-class" ] }, { "page": "NeuroVol", "title": "NeuroVol: 3D Neuroimaging Volume Class", "topics": [ "NeuroVol" ] }, { "page": "NeuroVol-class", "title": "NeuroVol Class", "topics": [ "NeuroVol-class" ] }, { "page": "NeuroVolSource-class", "title": "Constructor for NeuroVolSource", "topics": [ "NeuroVolSource" ] }, { "page": "NiftiExtension", "title": "Create a NIfTI Extension", "topics": [ "NiftiExtension" ] }, { "page": "NiftiExtension-class", "title": "NiftiExtension Class", "topics": [ "NiftiExtension-class", "show,NiftiExtension-method" ] }, { "page": "NiftiExtensionCodes", "title": "Known NIfTI Extension Codes", "topics": [ "NiftiExtensionCodes" ] }, { "page": "NiftiExtensionList-class", "title": "NiftiExtensionList Class", "topics": [ "NiftiExtensionList-class", "show,NiftiExtensionList-method" ] }, { "page": "NIFTIMetaInfo", "title": "Create NIFTI Format Metadata Object", "topics": [ "NIFTIMetaInfo" ] }, { "page": "None", "title": "Pre-defined null axis", "topics": [ "None" ] }, { "page": "not-methods", "title": "Logical Negation for Neuroimaging Volumes", "topics": [ "!,DenseNeuroVol-method", "!,SparseNeuroVol-method", "not-methods" ] }, { "page": "NullAxis", "title": "Pre-defined null axis set", "topics": [ "NullAxis" ] }, { "page": "num_clusters-methods", "title": "Number of Clusters", "topics": [ "num_clusters", "num_clusters,ClusteredNeuroVec-method", "num_clusters,ClusteredNeuroVol-method" ] }, { "page": "numericOrMatrix-class", "title": "numericOrMatrix Union", "topics": [ "numericOrMatrix-class" ] }, { "page": "orientation_utils", "title": "Orientation utility functions", "topics": [ "affine_to_axcodes", "affine_to_orientation", "apply_orientation", "axcodes_to_orientation", "orientation_inverse_affine", "orientation_to_axcodes", "orientation_transform", "orientation_utils" ] }, { "page": "OrientationList2D", "title": "Pre-defined 2D orientation configurations", "topics": [ "OrientationList2D" ] }, { "page": "OrientationList3D", "title": "Pre-defined 3D orientation configurations", "topics": [ "OrientationList3D" ] }, { "page": "origin-methods", "title": "Extract Image Origin", "topics": [ "origin", "origin,NeuroHyperVec-method", "origin,NeuroSpace-method", "origin,NeuroVec-method", "origin,NeuroVol-method" ] }, { "page": "parse_afni_extension", "title": "Parse AFNI Extension", "topics": [ "parse_afni_extension" ] }, { "page": "parse_extension", "title": "Parse NIfTI Extension Data", "topics": [ "parse_extension" ] }, { "page": "partition-methods", "title": "Partition an image into a set of disjoint clusters", "topics": [ "partition", "partition,DenseNeuroVol,numeric-method", "partition,LogicalNeuroVol,integer-method", "partition,LogicalNeuroVol,numeric-method" ] }, { "page": "patch_set", "title": "Generate a set of coordinate \"patches\" of fixed size from an image object.", "topics": [ "patch_set" ] }, { "page": "patch_set-methods", "title": "Create a patch set from a NeuroVol object", "topics": [ "patch_set,NeuroVol,numeric,LogicalNeuroVol-method", "patch_set,NeuroVol,numeric,missing-method" ] }, { "page": "perm_mat-methods", "title": "Extract permutation matrix associated with an image", "topics": [ "perm_mat", "perm_mat,AxisSet2D-method", "perm_mat,AxisSet3D-method", "perm_mat,NeuroSpace-method" ] }, { "page": "plot_checkerboard", "title": "Checkerboard comparison of two registered volumes", "topics": [ "plot_checkerboard" ] }, { "page": "plot_edge_overlay", "title": "Overlay fixed and moving edge maps on a background volume", "topics": [ "plot_edge_overlay" ] }, { "page": "plot_montage", "title": "Plot a montage of axial (or any-plane) slices using facetting", "topics": [ "plot_montage" ] }, { "page": "plot_ortho", "title": "Orthogonal three-plane view with optional crosshairs", "topics": [ "plot_ortho" ] }, { "page": "plot_overlay", "title": "Composite an overlay map on a structural background", "topics": [ "plot_overlay" ] }, { "page": "plot-methods", "title": "Plot a NeuroSlice", "topics": [ "plot,NeuroSlice,ANY-method", "plot,NeuroSlice-method", "plot,NeuroVol,missing-method", "plot,NeuroVol,NeuroVol-method", "plot,NeuroVol-method" ] }, { "page": "prepare_confounds", "title": "Prepare weighted nuisance projectors for each run", "topics": [ "prepare_confounds" ] }, { "page": "quaternToMatrix", "title": "Convert Quaternion Parameters to a Transformation Matrix", "topics": [ "quaternToMatrix" ] }, { "page": "random_searchlight", "title": "Create a spherical random searchlight iterator", "topics": [ "random_searchlight" ] }, { "page": "read_header", "title": "read header information of an image file", "topics": [ "read_header" ] }, { "page": "read_hyper_vec", "title": "Read a 5D image as a NeuroHyperVec", "topics": [ "read_hyper_vec" ] }, { "page": "read_image", "title": "read_image", "topics": [ "read_image" ] }, { "page": "read_meta_info-methods", "title": "Generic function to read image meta info given a file", "topics": [ "read_meta_info", "read_meta_info,AFNIFormat-method", "read_meta_info,NIFTIFormat-method" ] }, { "page": "read_vec", "title": "read_vec", "topics": [ "read_vec" ] }, { "page": "read_vol", "title": "Load a single 3D image volume from a file", "topics": [ "read_vol" ] }, { "page": "read_vol_list", "title": "read_vol_list", "topics": [ "read_vol_list" ] }, { "page": "reorient-methods", "title": "Remap the grid-to-world coordinates mapping of an image.", "topics": [ "reorient", "reorient,NeuroSpace,character-method" ] }, { "page": "resample-methods", "title": "Resample an Image to Match the Space of Another Image", "topics": [ "resample", "resample,ClusteredNeuroVol,NeuroSpace-method", "resample,ClusteredNeuroVol,NeuroVol-method", "resample,NeuroVol,NeuroSpace-method", "resample,NeuroVol,NeuroVol-method" ] }, { "page": "resample_to", "title": "Resample an image with readable method names", "topics": [ "resample_to" ] }, { "page": "resampled_searchlight", "title": "Create a resampled searchlight iterator", "topics": [ "bootstrap_searchlight", "resampled_searchlight" ] }, { "page": "resolve_cmap", "title": "Neuroimaging color palettes and helpers", "topics": [ "resolve_cmap" ] }, { "page": "ROI-class", "title": "ROI", "topics": [ "ROI-class" ] }, { "page": "ROICoords", "title": "Create ROI Coordinates Object", "topics": [ "ROICoords" ] }, { "page": "ROICoords-class", "title": "ROICoords", "topics": [ "ROICoords-class" ] }, { "page": "ROIVec", "title": "Create an instance of class 'ROIVec'", "topics": [ "ROIVec" ] }, { "page": "ROIVec-class", "title": "ROIVec", "topics": [ "ROIVec-class" ] }, { "page": "ROIVecWindow-class", "title": "ROIVecWindow", "topics": [ "ROIVecWindow-class" ] }, { "page": "ROIVol", "title": "Create ROI Volume Object", "topics": [ "ROIVol" ] }, { "page": "ROIVol-class", "title": "ROIVol", "topics": [ "ROIVol-class" ] }, { "page": "ROIVolWindow-class", "title": "ROIVolWindow", "topics": [ "ROIVolWindow-class" ] }, { "page": "scale", "title": "Generic Scale Method", "topics": [ "scale" ] }, { "page": "scale_fill_neuro", "title": "A ggplot2 fill scale with neuroimaging-friendly defaults", "topics": [ "scale_fill_neuro" ] }, { "page": "scale_series-methods", "title": "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.", "topics": [ "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" ] }, { "page": "searchlight", "title": "Create an exhaustive searchlight iterator", "topics": [ "searchlight" ] }, { "page": "searchlight_coords", "title": "Create an exhaustive searchlight iterator for voxel coordinates using spherical_roi", "topics": [ "searchlight_coords" ] }, { "page": "searchlight_shape_functions", "title": "Convenience shape generators for 'resampled_searchlight()'", "topics": [ "blobby_shape", "cube_shape", "ellipsoid_shape", "searchlight_shape_functions" ] }, { "page": "searchlight-methods", "title": "Searchlight Analysis Methods", "topics": [ "searchlight-methods" ] }, { "page": "series-methods", "title": "Extract one or more series from object", "topics": [ "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" ] }, { "page": "series_roi", "title": "Extract time series from specific voxel coordinates and return as ROI object", "topics": [ "series_roi" ] }, { "page": "show-methods", "title": "Show method for NamedAxis objects", "topics": [ "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" ] }, { "page": "simulate_fmri", "title": "Simulate fMRI Data", "topics": [ "simulate_fmri" ] }, { "page": "slice-methods", "title": "Extract image slice", "topics": [ "slice", "slice,NeuroVol,numeric,NeuroSpace,AxisSet3D-method", "slice,NeuroVol,numeric,numeric,missing-method" ] }, { "page": "slices-methods", "title": "Extract an ordered series of 2D slices from a 3D or 4D object", "topics": [ "slices", "slices,NeuroVol-method" ] }, { "page": "space-methods", "title": "Extract Geometric Properties of an Image", "topics": [ "space", "space,ClusteredNeuroVec-method", "space,IndexLookupVol-method", "space,NeuroHyperVec-method", "space,NeuroObj-method", "space,NeuroSpace-method", "space,ROICoords-method" ] }, { "page": "space_utils", "title": "Space utility functions", "topics": [ "output_aligned_space", "slice2volume", "slice_to_volume_affine", "space_utils", "vox2out_vox" ] }, { "page": "spacing-methods", "title": "Extract Voxel Dimensions of an Image", "topics": [ "spacing", "spacing,NeuroHyperVec-method", "spacing,NeuroObj-method", "spacing,NeuroSpace-method", "spacing,ROICoords-method" ] }, { "page": "SparseNeuroVec-class", "title": "SparseNeuroVec Class", "topics": [ "SparseNeuroVec", "SparseNeuroVec-class" ] }, { "page": "SparseNeuroVecSource-class", "title": "SparseNeuroVecSource Class", "topics": [ "SparseNeuroVecSource-class" ] }, { "page": "SparseNeuroVol-class", "title": "SparseNeuroVol Class", "topics": [ "SparseNeuroVol", "SparseNeuroVol-class" ] }, { "page": "spatial-filter", "title": "Spatial Filtering Methods for Neuroimaging Data", "topics": [ "spatial-filter" ] }, { "page": "spherical_roi", "title": "Create a Spherical Region of Interest", "topics": [ "spherical_roi" ] }, { "page": "spherical_roi_set", "title": "Create Multiple Spherical Regions of Interest", "topics": [ "spherical_roi_set" ] }, { "page": "split_blocks-methods", "title": "Cut a vector-valued object into a list of sub-blocks", "topics": [ "split_blocks", "split_blocks,NeuroVec,factor-method", "split_blocks,NeuroVec,integer-method" ] }, { "page": "split_clusters-methods", "title": "Cut an object into a list of spatial or spatiotemporal clusters", "topics": [ "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" ] }, { "page": "split_fill-methods", "title": "Fill Disjoint Sets of Values with the Output of a Function", "topics": [ "split_fill", "split_fill,NeuroVol,factor,function-method" ] }, { "page": "split_reduce-methods", "title": "Summarize Subsets of an Object by Splitting by Row and Applying a Summary Function", "topics": [ "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" ] }, { "page": "split_scale-methods", "title": "Center and/or Scale Row-subsets of a Matrix or Matrix-like Object", "topics": [ "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" ] }, { "page": "square_roi", "title": "Create a square region of interest", "topics": [ "square_roi" ] }, { "page": "strip_extension-methods", "title": "Generic function to strip extension from file name, given a 'FileFormat' instance.", "topics": [ "strip_extension", "strip_extension,FileFormat,character-method" ] }, { "page": "sub_clusters", "title": "Select a Subset of Clusters", "topics": [ "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" ] }, { "page": "sub_vector-methods", "title": "Generic function to extract a sub-vector from a 'NeuroVec' object.", "topics": [ "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" ] }, { "page": "Summary-methods", "title": "Summary Methods for Neuroimaging Objects", "topics": [ "Summary,DenseNeuroVol-method", "Summary,SparseNeuroVec-method", "Summary,SparseNeuroVol-method", "Summary-methods" ] }, { "page": "summary-neuro-methods", "title": "Summary of Neuroimaging Objects", "topics": [ "summary,DenseNeuroVec-method", "summary,NeuroVol-method", "summary,SparseNeuroVec-method", "summary-neuro-methods" ] }, { "page": "temporal_access-methods", "title": "Extract full sparse rows across time.", "topics": [ "temporal_access", "temporal_access,BigNeuroVec,integer-method", "temporal_access,BigNeuroVec,numeric-method", "temporal_access,SparseNeuroVec,integer-method", "temporal_access,SparseNeuroVec,numeric-method" ] }, { "page": "theme_neuro", "title": "A minimal, publication-friendly theme for image slices", "topics": [ "theme_neuro" ] }, { "page": "TIME", "title": "Time axis", "topics": [ "TIME" ] }, { "page": "TimeAxis", "title": "Time axis set", "topics": [ "TimeAxis" ] }, { "page": "trans-methods", "title": "Extract image coordinate transformation", "topics": [ "trans", "trans,MetaInfo-method", "trans,NeuroHyperVec-method", "trans,NeuroObj-method", "trans,NeuroSpace-method", "trans,NIFTIMetaInfo-method" ] }, { "page": "values-methods", "title": "Extract Data Values of an Object", "topics": [ "values", "values,ClusteredNeuroVec-method", "values,DenseNeuroVol-method", "values,ROIVec-method", "values,ROIVol-method", "values,SparseNeuroVol-method" ] }, { "page": "vec_from_vols", "title": "Create NeuroVec from list of NeuroVol objects", "topics": [ "vec_from_vols" ] }, { "page": "vectors-methods", "title": "Extract an ordered list of 1D vectors.", "topics": [ "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" ] }, { "page": "vols-methods", "title": "Extract an ordered series of 3D volumes.", "topics": [ "vols", "vols,NeuroVec,missing-method", "vols,NeuroVec,numeric-method" ] }, { "page": "volume_labels-methods", "title": "Get per-volume labels for a 'NeuroVec'.", "topics": [ "volume_labels", "volume_labels,NeuroVec-method" ] }, { "page": "voxels-methods", "title": "extract voxel coordinates", "topics": [ "voxels", "voxels,Kernel-method" ] }, { "page": "which_dim-methods", "title": "Find Dimensions of a Given Axis", "topics": [ "which_dim", "which_dim,NeuroSpace,NamedAxis-method" ] }, { "page": "write_elements-methods", "title": "Write a sequence of elements from an input source", "topics": [ "write_elements", "write_elements,BinaryWriter,numeric-method" ] }, { "page": "write_vec-methods", "title": "Write a 4d image vector to disk", "topics": [ "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" ] }, { "page": "write_vol-methods", "title": "Write a 3d image volume to disk", "topics": [ "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" ] } ], "_readme": "https://github.com/bbuchsbaum/neuroim2/raw/HEAD/README.md", "_rundeps": [ "assertthat", "bigassertr", "bigparallelr", "bigstatsr", "bit", "cachem", "cli", "codetools", "cowplot", "cpp11", "dbscan", "deflist", "digest", "doParallel", "farver", "fastmap", "ff", "flock", "foreach", "future", "future.apply", "generics", "ggplot2", "globals", "glue", "gtable", "isoband", "iterators", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "Matrix", "memoise", "mmap", "parallelly", "patchwork", "pillar", "pkgconfig", "ps", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "RhpcBLASctl", "rlang", "rmio", "RNifti", "RNiftyReg", "RSpectra", "S7", "scales", "stringi", "stringr", "tibble", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "ImageVolumes.Rmd", "filename": "ImageVolumes.html", "title": "Advanced 3D Volume Patterns", "engine": "knitr::rmarkdown", "headings": [ "Read one volume to establish context", "Coordinate conversion and spatial metadata", "Masks and LogicalNeuroVol", "Constructing volumes manually", "Slicing and quick visualization", "Reorienting and resampling", "Downsampling", "Writing a NIFTI formatted image volume" ], "created": "2018-07-04 13:09:25", "modified": "2026-04-10 20:02:18", "commits": 18 }, { "source": "NeuroVector.Rmd", "filename": "NeuroVector.html", "title": "Advanced NeuroVec Patterns", "engine": "knitr::rmarkdown", "headings": [ "Working with neuroimaging time-series data", "Reading multiple four-dimensional images", "Creating a NeuroVec from an in-memory array", "Time-series transforms: z-scoring and summary volumes", "Concatenating along time", "Dense ↔ sparse workflows", "Writing vectors to disk", "Putting it together with an ROI" ], "created": "2019-02-08 14:55:16", "modified": "2026-04-23 14:37:16", "commits": 20 }, { "source": "regionOfInterest.Rmd", "filename": "regionOfInterest.html", "title": "Advanced ROI Construction", "engine": "knitr::rmarkdown", "headings": [ "ROI types in neuroim2", "Quick start", "Basic ROI operations", "Creating a Spherical ROI", "Performance Note: C++ vs Pure R Implementation", "Creating a Spherical ROI Around Real-World Coordinates", "Creating Multiple Spherical ROIs Efficiently", "Creating Cuboid and Square ROIs", "Cuboid ROIs (3D boxes)", "Square ROIs (2D in 3D space)", "Working with ROI Data", "Converting ROIs to Sparse Volumes", "Using ROIVec for 4D ROI Data", "Image Patches", "Advanced ROI Techniques", "Custom Weighted ROIs with Kernels", "Working with ClusteredNeuroVec for Parcellated Data", "ROI Set Operations", "Best Practices and Performance", "Memory Management", "Choosing ROI Sizes", "Parallel Processing Tips", "Troubleshooting and Tips", "Common Issues and Solutions", "Issue: ROI extends outside brain mask", "Issue: Different coordinate systems", "See Also" ], "created": "2017-11-02 02:12:50", "modified": "2026-04-23 14:37:16", "commits": 19 }, { "source": "pipelines.Rmd", "filename": "pipelines.html", "title": "Advanced Split, Map, and 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