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  "Title": "Neuroimaging Atlases and Parcellations",
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  "License": "MIT + file LICENSE",
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  "Repository": "https://bbuchsbaum.r-universe.dev",
  "Date/Publication": "2026-06-05 15:46:20 UTC",
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    {
      "page": "coord_spaces",
      "title": "Standard Coordinate Space Identifiers",
      "topics": [
        "coord_spaces"
      ]
    },
    {
      "page": "coordinate_spaces",
      "title": "Coordinate Space Transforms for Neuroimaging Templates",
      "topics": [
        "coordinate_spaces"
      ]
    },
    {
      "page": "create_templateflow",
      "title": "Create a TemplateFlow Interface Object",
      "topics": [
        "create_templateflow"
      ]
    },
    {
      "page": "dilate_atlas",
      "title": "Dilate Atlas Parcellation Boundaries",
      "topics": [
        "dilate_atlas"
      ]
    },
    {
      "page": "filter_atlas",
      "title": "Filter Atlas by ROI Attributes",
      "topics": [
        "filter_atlas",
        "filter_atlas.atlas"
      ]
    },
    {
      "page": "fsaverage",
      "title": "Surface geometry for the fsaverage6 atlas",
      "topics": [
        "fsaverage"
      ]
    },
    {
      "page": "get_aseg_atlas",
      "title": "Get the FreeSurfer Subcortical Atlas (ASEG)",
      "topics": [
        "get_aseg_atlas"
      ]
    },
    {
      "page": "get_atlas",
      "title": "Load an Atlas by Registered ID",
      "topics": [
        "get_atlas"
      ]
    },
    {
      "page": "get_brainnetome_atlas",
      "title": "Load Brainnetome 246-Region Atlas",
      "topics": [
        "get_brainnetome_atlas"
      ]
    },
    {
      "page": "get_fsl_atlas",
      "title": "FSL Atlas Loaders",
      "topics": [
        "get_fsl_atlas"
      ]
    },
    {
      "page": "get_ggseg_atlas",
      "title": "Get ggseg-Compatible Schaefer Atlas",
      "topics": [
        "get_ggseg_atlas"
      ]
    },
    {
      "page": "get_glasser_atlas",
      "title": "Load Glasser Atlas",
      "topics": [
        "get_glasser_atlas"
      ]
    },
    {
      "page": "get_harvard_oxford_atlas",
      "title": "Load a Harvard-Oxford Atlas",
      "topics": [
        "get_harvard_oxford_atlas",
        "get_harvard_oxford_cortical_atlas",
        "get_harvard_oxford_cortical_subcortical_atlas",
        "get_harvard_oxford_subcortical_atlas"
      ]
    },
    {
      "page": "get_hipp_atlas",
      "title": "Extract Hippocampal Parcellation",
      "topics": [
        "get_hipp_atlas"
      ]
    },
    {
      "page": "get_julich_brain_atlas",
      "title": "Load a Julich-Brain FSL Atlas",
      "topics": [
        "get_julich_brain_atlas"
      ]
    },
    {
      "page": "get_olsen_mtl",
      "title": "Load Olsen MTL Atlas",
      "topics": [
        "get_olsen_mtl"
      ]
    },
    {
      "page": "get_roi",
      "title": "Extract a region of interest (ROI) from an atlas",
      "topics": [
        "get_roi",
        "get_roi.atlas"
      ]
    },
    {
      "page": "get_schaefer_atlas",
      "title": "Load Schaefer Brain Parcellation Atlas",
      "topics": [
        "get_schaefer_atlas",
        "sy_1000_17",
        "sy_1000_7",
        "sy_100_17",
        "sy_100_7",
        "sy_200_17",
        "sy_200_7",
        "sy_300_17",
        "sy_300_7",
        "sy_400_17",
        "sy_400_7",
        "sy_500_17",
        "sy_500_7",
        "sy_600_17",
        "sy_600_7",
        "sy_700_17",
        "sy_700_7",
        "sy_800_17",
        "sy_800_7",
        "sy_900_17",
        "sy_900_7"
      ]
    },
    {
      "page": "get_schaefer_surfatlas",
      "title": "Load Surface-Based Schaefer Atlas",
      "topics": [
        "get_schaefer_surfatlas"
      ]
    },
    {
      "page": "get_space_transform",
      "title": "Get Transform Matrix Between Coordinate Spaces",
      "topics": [
        "get_space_transform"
      ]
    },
    {
      "page": "get_subcortical_atlas",
      "title": "Load harmonized subcortical atlases via TemplateFlow",
      "topics": [
        "get_subcortical_atlas"
      ]
    },
    {
      "page": "get_surface_coordinate_space",
      "title": "Get Coordinate Space for a Surface Template",
      "topics": [
        "get_surface_coordinate_space"
      ]
    },
    {
      "page": "get_template",
      "title": "Fetch a Template from TemplateFlow",
      "topics": [
        "get_surface_template",
        "get_template"
      ]
    },
    {
      "page": "get_visfatlas",
      "title": "visfAtlas Probabilistic Functional Visual Atlas (volume)",
      "topics": [
        "get_visfatlas"
      ]
    },
    {
      "page": "get_visual_atlas",
      "title": "Early Visual Cortex Atlas (V1-V5, cytoarchitectonic)",
      "topics": [
        "get_visual_atlas"
      ]
    },
    {
      "page": "get_wang_atlas",
      "title": "Wang (2015) Probabilistic Visual Topography Atlas",
      "topics": [
        "get_wang_atlas"
      ]
    },
    {
      "page": "get_wang_prob_atlas",
      "title": "Wang (2015) Full Per-Area Probability Volumes (Princeton ProbAtlas_v4)",
      "topics": [
        "get_wang_prob_atlas",
        "print.wang_prob_paths"
      ]
    },
    {
      "page": "ggseg_schaefer",
      "title": "Create Interactive Schaefer Atlas Visualization",
      "topics": [
        "ggseg_schaefer"
      ]
    },
    {
      "page": "glasser_surf",
      "title": "Glasser Surface Atlas (fsaverage)",
      "topics": [
        "glasser_surf"
      ]
    },
    {
      "page": "infer_design_var_type",
      "title": "Infer Design Variable Type",
      "topics": [
        "infer_design_var_type"
      ]
    },
    {
      "page": "install_templateflow",
      "title": "Install Templateflow (DEPRECATED)",
      "topics": [
        "install_templateflow"
      ]
    },
    {
      "page": "launch_cluster_explorer",
      "title": "Launch Cluster Explorer in Interactive Session",
      "topics": [
        "launch_cluster_explorer"
      ]
    },
    {
      "page": "list_atlases",
      "title": "List Registered Atlases",
      "topics": [
        "list_atlases"
      ]
    },
    {
      "page": "load_surface_template",
      "title": "Load a surface template as a neurosurf geometry",
      "topics": [
        "load_surface_template"
      ]
    },
    {
      "page": "map_atlas",
      "title": "Map values to an atlas",
      "topics": [
        "map_atlas",
        "map_atlas.atlas",
        "map_atlas.glasser",
        "map_atlas.schaefer"
      ]
    },
    {
      "page": "map_to_schaefer",
      "title": "Map Values to Schaefer Atlas Format",
      "topics": [
        "map_to_schaefer"
      ]
    },
    {
      "page": "merge_atlases",
      "title": "Merge Two Brain Atlases",
      "topics": [
        "merge_atlases"
      ]
    },
    {
      "page": "MNI152_to_MNI305",
      "title": "MNI152 to MNI305 Affine Transform Matrix",
      "topics": [
        "MNI152_to_MNI305"
      ]
    },
    {
      "page": "MNI305_to_MNI152",
      "title": "MNI305 to MNI152 Affine Transform Matrix",
      "topics": [
        "MNI305_to_MNI152"
      ]
    },
    {
      "page": "needs_coord_transform",
      "title": "Check if a Coordinate Transform is Needed",
      "topics": [
        "needs_coord_transform"
      ]
    },
    {
      "page": "needs_template_warp",
      "title": "Check if a Nonlinear Template Warp is Needed",
      "topics": [
        "needs_template_warp"
      ]
    },
    {
      "page": "needs_transform",
      "title": "Check if Transform is Needed Between Spaces",
      "topics": [
        "needs_transform"
      ]
    },
    {
      "page": "network_anchor_hues",
      "title": "Assign harmonic anchor hues to networks",
      "topics": [
        "network_anchor_hues"
      ]
    },
    {
      "page": "new_atlas_ref",
      "title": "Atlas Reference Metadata",
      "topics": [
        "new_atlas_ref"
      ]
    },
    {
      "page": "olsen_mtl",
      "title": "Olsen Medial Temporal Lobe Atlas",
      "topics": [
        "olsen_mtl"
      ]
    },
    {
      "page": "parcel_data",
      "title": "Parcel-Level Data Container",
      "topics": [
        "parcel_data"
      ]
    },
    {
      "page": "parcel_values",
      "title": "Extract Parcel Values Aligned to an Atlas",
      "topics": [
        "parcel_values"
      ]
    },
    {
      "page": "plot_brain",
      "title": "Plot Brain Surface Atlas",
      "topics": [
        "plot_brain"
      ]
    },
    {
      "page": "plot_brain_grid",
      "title": "Multi-panel Brain Plot Grid",
      "topics": [
        "plot_brain_grid"
      ]
    },
    {
      "page": "plot_glasser",
      "title": "Plot Glasser Atlas Values",
      "topics": [
        "plot_glasser"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Plot Glasser Atlas",
      "topics": [
        "plot-methods",
        "plot.atlas",
        "plot.glasser",
        "plot.surfatlas"
      ]
    },
    {
      "page": "print-methods",
      "title": "Print Methods for neuroatlas Objects",
      "topics": [
        "print-methods",
        "print.atlas",
        "print.atlas_provenance",
        "print.glasser",
        "print.schaefer"
      ]
    },
    {
      "page": "print.atlas_alignment",
      "title": "Print Method for Atlas Alignment Results",
      "topics": [
        "print.atlas_alignment"
      ]
    },
    {
      "page": "print.atlas_ref",
      "title": "Print Method for Atlas References",
      "topics": [
        "print.atlas_ref"
      ]
    },
    {
      "page": "print.atlas_transform_plan",
      "title": "Print Method for Transform Plans",
      "topics": [
        "print.atlas_transform_plan"
      ]
    },
    {
      "page": "print.templateflow",
      "title": "Print a TemplateFlow Object",
      "topics": [
        "print.templateflow"
      ]
    },
    {
      "page": "project_surface_view",
      "title": "Project Surface Vertices to a Canonical 2D View",
      "topics": [
        "project_surface_view"
      ]
    },
    {
      "page": "query_coord",
      "title": "Query Atlas Labels by Coordinate",
      "topics": [
        "query_coord",
        "query_vox"
      ]
    },
    {
      "page": "query_point",
      "title": "Look Up Atlas Regions at MNI Coordinates",
      "topics": [
        "query_point"
      ]
    },
    {
      "page": "read_parcel_data",
      "title": "Read a `parcel_data` Object from Disk",
      "topics": [
        "read_parcel_data"
      ]
    },
    {
      "page": "reduce_atlas",
      "title": "Reduce a NeuroVol or NeuroVec by an Atlas",
      "topics": [
        "reduce_atlas",
        "reduce_atlas.atlas"
      ]
    },
    {
      "page": "reduce_atlas_vec",
      "title": "Reduce a NeuroVec by an Atlas to a ClusteredNeuroVec",
      "topics": [
        "reduce_atlas_vec",
        "reduce_atlas_vec.atlas"
      ]
    },
    {
      "page": "resample",
      "title": "Resample Volume to New Space",
      "topics": [
        "resample"
      ]
    },
    {
      "page": "roi_attributes",
      "title": "List Available ROI Attributes",
      "topics": [
        "roi_attributes",
        "roi_attributes.atlas"
      ]
    },
    {
      "page": "roi_colors_embedding",
      "title": "Embedding-based palette with smooth gradients",
      "topics": [
        "roi_colors_embedding"
      ]
    },
    {
      "page": "roi_colors_maximin_view",
      "title": "Slice-aware maximin palette for ROIs",
      "topics": [
        "roi_colors_maximin_view"
      ]
    },
    {
      "page": "roi_colors_network_harmony",
      "title": "Network-harmonic palette with neighbour separation",
      "topics": [
        "roi_colors_network_harmony"
      ]
    },
    {
      "page": "roi_colors_rule_hcl",
      "title": "Deterministic HCL palette with harmonic variation",
      "topics": [
        "roi_colors_rule_hcl"
      ]
    },
    {
      "page": "roi_metadata",
      "title": "ROI Metadata Functions",
      "topics": [
        "roi_metadata",
        "roi_metadata.atlas"
      ]
    },
    {
      "page": "schaefer_surf",
      "title": "Schaefer Surface Atlas",
      "topics": [
        "schaefer_surf"
      ]
    },
    {
      "page": "schaefer_surf_options",
      "title": "List supported Schaefer surface atlas variants",
      "topics": [
        "schaefer_surf_options"
      ]
    },
    {
      "page": "show_templateflow_cache_path",
      "title": "Show neuroatlas TemplateFlow Cache Path",
      "topics": [
        "show_templateflow_cache_path"
      ]
    },
    {
      "page": "space_transform_manifest",
      "title": "Space Transform Manifest",
      "topics": [
        "space_transform_manifest"
      ]
    },
    {
      "page": "spin_test",
      "title": "Spin Test for Spatial Correlation Significance",
      "topics": [
        "spin_test"
      ]
    },
    {
      "page": "sub_atlas",
      "title": "Select a Subset of Atlas Regions",
      "topics": [
        "sub_atlas",
        "sub_atlas.atlas"
      ]
    },
    {
      "page": "subcortical_atlas_options",
      "title": "Subcortical Atlas Options (TemplateFlow-backed)",
      "topics": [
        "subcortical_atlas_options"
      ]
    },
    {
      "page": "template_to_coord_space",
      "title": "Get Coordinate Space for Any Template",
      "topics": [
        "template_to_coord_space"
      ]
    },
    {
      "page": "tflow_files",
      "title": "Find TemplateFlow Files Matching Metadata Criteria",
      "topics": [
        "tflow_files"
      ]
    },
    {
      "page": "tflow_spaces",
      "title": "List Available TemplateFlow Template Spaces",
      "topics": [
        "tflow_spaces"
      ]
    },
    {
      "page": "transform_coords",
      "title": "Transform Coordinates Between Spaces",
      "topics": [
        "transform_coords"
      ]
    },
    {
      "page": "transform_vertices_to_volume",
      "title": "Transform Surface Vertices to Volume Space",
      "topics": [
        "transform_vertices_to_volume"
      ]
    },
    {
      "page": "validate_atlas_ref",
      "title": "Validate an Atlas Reference",
      "topics": [
        "validate_atlas_ref"
      ]
    },
    {
      "page": "validate_parcel_data",
      "title": "Validate a Parcel-Level Data Object",
      "topics": [
        "validate_parcel_data"
      ]
    },
    {
      "page": "write_parcel_data",
      "title": "Write a `parcel_data` Object to Disk",
      "topics": [
        "write_parcel_data"
      ]
    }
  ],
  "_readme": "https://github.com/bbuchsbaum/neuroatlas/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "assertthat",
    "base64enc",
    "bigassertr",
    "bigparallelr",
    "bigstatsr",
    "bit",
    "bit64",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "clipr",
    "codetools",
    "colorplane",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "dbscan",
    "deflist",
    "digest",
    "doParallel",
    "downloader",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "ff",
    "flock",
    "FNN",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "fs",
    "future",
    "future.apply",
    "gdtools",
    "generics",
    "ggiraph",
    "ggplot2",
    "gifti",
    "globals",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr2",
    "igraph",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "mmap",
    "neuroim2",
    "neurosurf",
    "openssl",
    "parallelly",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "ps",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppParallel",
    "readr",
    "rgl",
    "RhpcBLASctl",
    "rlang",
    "rmarkdown",
    "rmio",
    "Rnanoflann",
    "RNifti",
    "RNiftyReg",
    "roptim",
    "RSpectra",
    "Rvcg",
    "S7",
    "sass",
    "scales",
    "scico",
    "stringi",
    "stringr",
    "sys",
    "systemfonts",
    "templateflow",
    "tibble",
    "tidyselect",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xml2",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "atlas-visualization.Rmd",
      "filename": "atlas-visualization.html",
      "title": "Atlas Visualization with Optimal Colours",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Quick Start",
        "Colour Algorithms",
        "rule_hcl (default)",
        "maximin_view",
        "network_harmony",
        "embedding",
        "Custom Colours",
        "Named vector",
        "Pre-computed tibble",
        "Programmatic Colour Access",
        "Controlling Slice Count",
        "Surface Figures with Layout Control",
        "Existing Visualisation Tools"
      ],
      "created": "2026-02-09 16:35:26",
      "modified": "2026-04-23 14:57:23",
      "commits": 4
    },
    {
      "source": "surface-panels.Rmd",
      "filename": "surface-panels.html",
      "title": "Composing Surface Panel Figures",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What problem are we solving?",
        "What do you need before you start?",
        "How do you build one polished panel figure?",
        "How do you compare several maps with one legend?",
        "What do the default panel labels mean?",
        "Which layout controls are worth remembering?",
        "Where should you go next?"
      ],
      "created": "2026-04-23 14:57:23",
      "modified": "2026-04-23 14:57:23",
      "commits": 1
    },
    {
      "source": "neuroatlas-overview.Rmd",
      "filename": "neuroatlas-overview.html",
      "title": "Getting Started with neuroatlas",
      "author": "neuroatlas Dev Team",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Loading Atlases",
        "Schaefer Cortical Atlas",
        "Glasser Multi-Modal Parcellation",
        "FreeSurfer ASEG Subcortical Atlas",
        "Olsen Medial Temporal Lobe Atlas",
        "Resampling Atlases to Different Spaces",
        "Working with Regions of Interest",
        "Extracting Specific ROIs",
        "Reducing Data by Atlas Regions",
        "Mapping Values to Atlas Regions",
        "Visualization",
        "Using ggseg for 2D Brain Plots",
        "Interactive 3D Visualization (Glasser)",
        "Combining and Dilating Atlases",
        "Merging Multiple Atlases",
        "Dilating Atlas Parcels",
        "Surface-Based Atlases",
        "Common Workflows",
        "ROI-Based Analysis Pipeline",
        "Multi-Atlas Comparison",
        "Network-Based Analysis",
        "Tips and Best Practices",
        "Summary"
      ],
      "created": "2025-06-05 01:20:46",
      "modified": "2026-02-20 12:02:19",
      "commits": 5
    },
    {
      "source": "surface-parcellations.Rmd",
      "filename": "surface-parcellations.html",
      "title": "Surface Parcellations with neurosurf",
      "author": "neuroatlas Dev Team",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What this vignette covers",
        "Discovering available surface templates",
        "Schaefer surface atlases",
        "Using TemplateFlow spaces (when available)",
        "Attaching your own values",
        "Glasser MMP1.0 surface atlas (when available)",
        "What’s in the data slot?",
        "Saving / reusing",
        "Sanity check: parcel surface renders",
        "Loading raw surface geometry from TemplateFlow",
        "Downloading surfaces to a local folder",
        "Common workflows",
        "Static figure layout and annotations",
        "Dense vertex-wise overlays",
        "Automatic NeuroVol projection",
        "Notes on dependencies"
      ],
      "created": "2025-12-01 17:20:15",
      "modified": "2026-04-23 14:57:23",
      "commits": 6
    },
    {
      "source": "surface-templates.Rmd",
      "filename": "surface-templates.html",
      "title": "Surface Templates: Geometry vs. Data",
      "author": "neuroatlas Dev Team",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Why this vignette",
        "Quick reference",
        "Fetching geometry only",
        "Both hemispheres at once",
        "Attaching per-vertex data",
        "Getting labeled surfaces (parcellations)",
        "When TemplateFlow is required",
        "Common patterns",
        "Sanity check: surface renders",
        "Template roster & snapshots",
        "Batch snapshot script (run locally)"
      ],
      "created": "2025-12-01 17:20:15",
      "modified": "2026-02-20 12:02:19",
      "commits": 3
    },
    {
      "source": "working-with-templateflow.Rmd",
      "filename": "working-with-templateflow.html",
      "title": "Working with TemplateFlow in neuroatlas",
      "author": "neuroatlas Dev Team",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started: The templateflow Object",
        "Discovering Templates and Metadata",
        "Listing Available Template Spaces",
        "Discovering Volumetric Templates",
        "Discovering Surface Templates",
        "Troubleshooting",
        "Fetching Templates with get_template()",
        "Basic Retrieval (Volumetric Data)",
        "Fetching Other Variants (e.g., Masks)",
        "Tissue Probability (GM/WM/CSF)",
        "Getting File Paths Only",
        "Vectorized Retrieval",
        "Key Parameters for get_template()",
        "Typed Helper Functions",
        "Volumetric Data with get_volume_template()",
        "Surface Data with get_surface_template()",
        "Downloading Templates to a Local Folder",
        "Copy from TemplateFlow cache",
        "Download specific surfaces with get_surface_template()",
        "Bulk download helper",
        "Caching Behavior",
        "Integration with Other neuroatlas Functions",
        "Summary",
        "Further Information"
      ],
      "created": "2025-05-17 13:36:26",
      "modified": "2026-02-20 12:02:19",
      "commits": 5
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