Package index • neuroatlas

Atlas loaders and discovery

atlas_registry: Atlas Registry
brainnetome_labels(): Brainnetome Atlas Label Table
get_aseg_atlas(): Get the FreeSurfer Subcortical Atlas (ASEG)
get_atlas(): Load an Atlas by Registered ID
get_brainnetome_atlas(): Load Brainnetome 246-Region Atlas
get_fsl_atlas(): FSL Atlas Loaders
get_ggseg_atlas(): Get ggseg-Compatible Schaefer Atlas
get_glasser_atlas(): Load Glasser Atlas
get_harvard_oxford_atlas() get_harvard_oxford_cortical_atlas() get_harvard_oxford_subcortical_atlas() get_harvard_oxford_cortical_subcortical_atlas(): Load a Harvard-Oxford Atlas
get_hcpex_atlas(): Load the Extended HCP Atlas (HCPex)
get_hipp_atlas(): Extract Hippocampal Parcellation
get_julich_brain_atlas(): Load a Julich-Brain FSL Atlas
get_olsen_mtl(): Load Olsen MTL Atlas
get_roi(<surfatlas>): Extract regions of interest from a surface atlas
get_roi(): Extract a region of interest (ROI) from an atlas
get_schaefer_atlas() sy_100_7() sy_100_17() sy_200_7() sy_200_17() sy_300_7() sy_300_17() sy_400_7() sy_400_17() sy_500_7() sy_500_17() sy_600_7() sy_600_17() sy_700_7() sy_700_17() sy_800_7() sy_800_17() sy_900_7() sy_900_17() sy_1000_7() sy_1000_17(): Load Schaefer Brain Parcellation Atlas
get_schaefer_surfatlas(): Load Surface-Based Schaefer Atlas
get_subcortical_atlas(): Load harmonized subcortical atlases via TemplateFlow
get_visfatlas(): visfAtlas Probabilistic Functional Visual Atlas (volume)
get_visual_atlas(): Early Visual Cortex Atlas (V1-V5, cytoarchitectonic)
get_wang_atlas(): Wang (2015) Probabilistic Visual Topography Atlas
get_wang_prob_atlas() print(<wang_prob_paths>): Wang (2015) Full Per-Area Probability Volumes (Princeton ProbAtlas_v4)
glasser_surf(): Glasser Surface Atlas (fsaverage)
olsen_mtl: Olsen Medial Temporal Lobe Atlas
schaefer_surf(): Schaefer Surface Atlas
schaefer_surf_options(): List supported Schaefer surface atlas variants

Atlas identity and provenance

atlas_artifacts(): Get Atlas Artifact Metadata
atlas_family(): Atlas Family Convenience Accessor
atlas_history(): Get Atlas Processing History
atlas_metadata() template_metadata() validate_resource_metadata() print(<NeuroResourceMetadata>): Atlas and Template Metadata
atlas_provenance() atlas_artifacts(<atlas>) atlas_artifacts(<default>) atlas_history(<atlas>) atlas_history(<default>): Atlas Provenance Accessors
atlas_ref(): Atlas Reference Accessor
new_atlas_ref(): Atlas Reference Metadata
validate_atlas(): Validate an Atlas Object
validate_atlas_ref(): Validate an Atlas Reference

Regions and parcel data

align_parcel_values(): Align a Parcel Value Column to an Atlas
as_parcel_data(): Convert an Object to `parcel_data`
atlas_alignment(): Atlas Alignment Lookup
atlas_citations() template_citations(): Bibliographic References for an Atlas or Template
new_atlas() new_surfatlas(): Atlas Constructor and Validator
atlas_download: Download Helpers for Atlas Loaders
atlas_roi_colors(): Assign optimal colours to atlas regions
batch_reduce(): Batch Reduce Multiple Volumes by an Atlas
build_conflict_edges(): Build slice-aware conflict edges between ROIs
.as_neurovol_unmemoised(): Internal Helper to Convert File Path to NeuroVol
.neuroatlas_cache_dir(): Get or Create neuroatlas Cache Directory
.neuroatlas_download(): Download an Atlas Asset (hard).
.neuroatlas_try_download(): Download an Atlas Asset (soft).
filter_atlas(): Filter Atlas by ROI Attributes
find_atlas_spec(): Look Up an Atlas Spec by ID or Alias
ggseg_schaefer(): Create Interactive Schaefer Atlas Visualization
`%where%`: Filter Atlas with Infix Operator
list_atlases(): List Registered Atlases
map_atlas(): Map values to an atlas
map_to_schaefer(): Map Values to Schaefer Atlas Format
merge_atlases(): Merge Two Brain Atlases
network_anchor_hues(): Assign harmonic anchor hues to networks
parcel_data(): Parcel-Level Data Container
parcel_values(): Extract Parcel Values Aligned to an Atlas
parcel_volume(): Expand Parcel Values to a Volumetric Atlas
project_cluster_overlay(): Project a Volume onto a Surface Atlas
read_parcel_data(): Read a `parcel_data` Object from Disk
reduce_atlas(): Reduce a NeuroVol or NeuroVec by an Atlas
reduce_atlas_vec(): Reduce a NeuroVec by an Atlas to a ClusteredNeuroVec
register_atlas(): Register an Atlas Spec
resample(): Resample Volume to New Space
roi_attributes(): List Available ROI Attributes
roi_colors_embedding(): Embedding-based palette with smooth gradients
roi_colors_maximin_view(): Slice-aware maximin palette for ROIs
roi_colors_network_harmony(): Network-harmonic palette with neighbour separation
roi_colors_rule_hcl(): Deterministic HCL palette with harmonic variation
roi_metadata(): ROI Metadata Functions
sub_atlas(): Select a Subset of Atlas Regions
subcortical_atlas_options(): Subcortical Atlas Options (TemplateFlow-backed)
tflow_files(): Find TemplateFlow Files Matching Metadata Criteria
validate_parcel_data(): Validate a Parcel-Level Data Object
write_parcel_data(): Write a `parcel_data` Object to Disk

Templates, domains and transforms

MNI152_to_MNI305: MNI152 to MNI305 Affine Transform Matrix
MNI305_to_MNI152: MNI305 to MNI152 Affine Transform Matrix
apply_surface_projection(): Sample a Volume onto an Explicit Cortical Projection
apply_surface_transform(): Apply a Domain-Bound Surface Transform
apply_template_transform(): Apply a Verified Template or Surface Transform
atlas_coord_space(): Atlas Coordinate-Space Convenience Accessor
atlas_space(): Atlas Template-Space Convenience Accessor
atlas_transform_manifest(): Atlas Transform Manifest
atlas_transform_plan(): Plan a Transform Between Spaces
`$`(<templateflow>): Access Attributes of the TemplateFlow Object (DEPRECATED)
check_templateflow(): Check TemplateFlow Installation Status
clear_templateflow_cache(): Clear neuroatlas TemplateFlow Cache
clear_transform_cache(): Clear Verified Transform Artifacts
coord_spaces: Standard Coordinate Space Identifiers
coordinate_spaces: Coordinate Space Transforms for Neuroimaging Templates
create_templateflow(): Create a TemplateFlow Interface Object
.check_templateflow_connectivity(): Check TemplateFlow Connectivity
.resolve_template_input(): Resolve Template Input to NeuroVol or NeuroSpace
fsaverage: Surface geometry for the fsaverage6 atlas
get_space_transform(): Get Transform Matrix Between Coordinate Spaces
get_surface_coordinate_space(): Get Coordinate Space for a Surface Template
get_surface_geometry(): Fetch Exact Pinned Surface Registration Geometry
get_surface_projection(): Resolve a Qualified Population Volume-to-Cortex Projection
get_surface_transform(): Build or Load a Directed Surface Transform
get_cifti_transform(): Bind Qualified Cortical Operators to a CIFTI Layout
apply_cifti_transform(): Apply Cortical Resampling While Preserving CIFTI Subcortex
read_cifti(): Read CIFTI-2 Dense Scalar or Label Maps
write_cifti(): Write CIFTI-2 Maps With Preserved Brain Models
replace_cifti_values(): Replace Values Without Changing CIFTI Brain Models
get_template() get_surface_template(): Fetch a Template from TemplateFlow
get_template_brainmask(): Get Brain Mask from Template (DEPRECATED)
get_template_csf(): Get CSF Probability Map (DEPRECATED)
get_template_gm(): Get Gray Matter Probability Map (DEPRECATED)
get_template_head(): Get Template Head Image (DEPRECATED)
get_template_legacy(): Access Templateflow Brain Templates (DEPRECATED - Legacy Signature)
get_template_probseg(): Get Tissue Probability Map from Template (DEPRECATED)
get_template_schaefer(): Get Schaefer Parcellation in Template Space (DEPRECATED)
get_template_transform(): Resolve and Load a Verified Template Transform
get_template_wm(): Get White Matter Probability Map (DEPRECATED)
install_templateflow(): Install Templateflow (DEPRECATED)
load_surface_template(): Load a surface template as a neurosurf geometry
names(<templateflow>): List Attributes of the TemplateFlow Object (DEPRECATED)
needs_coord_transform(): Check if a Coordinate Transform is Needed
needs_template_warp(): Check if a Nonlinear Template Warp is Needed
needs_transform(): Check if Transform is Needed Between Spaces
projection_diagnostics(): Inspect Coverage and Label Loss in a Cortical Projection
query_coord() query_vox(): Query Atlas Labels by Coordinate
ribbon_projection(): Declare Aligned White/Pial Ribbon Sampling
show_templateflow_cache_path(): Show neuroatlas TemplateFlow Cache Path
space_transform_manifest(): Space Transform Manifest
`[[`(<templateflow>): Access Attributes of the TemplateFlow Object using [[ (DEPRECATED)
surface_data(): Bind Vertex Values to an Exact Surface Domain
surface_domain(): Identify an Exact Surface Vertex Domain
surface_geometry(): Bind Registration Geometry to a Surface Domain
template_to_coord_space(): Get Coordinate Space for Any Template
templates(): List Available Templates
tflow_spaces(): List Available TemplateFlow Template Spaces
transform_atlas(): Transform a Volumetric Atlas to a Template or Cortical Surface
transform_cache_path(): Transform Artifact Cache Path
transform_coords(): Transform Coordinates Between Spaces
transform_vertices_to_volume(): Transform Surface Vertices to Volume Space

Visualization and exploration

build_brain_polygon_data(): Build brain polygon render data for a surface atlas
build_cluster_explorer_data(): Build Cluster Explorer Data
build_surface_polygon_data(): Build Surface Polygon Data for Rendering
cluster_explorer(): Launch Cluster Explorer Shiny App
infer_design_var_type(): Infer Design Variable Type
launch_cluster_explorer(): Launch Cluster Explorer in Interactive Session
plot_brain(): Plot Brain Surface Atlas
plot_brain_grid(): Multi-panel Brain Plot Grid
plot_glasser(): Plot Glasser Atlas Values
project_surface_view(): Project Surface Vertices to a Canonical 2D View
surface_anatomy(): Resolve an anatomical underlay for a surface atlas

Graphs and spatial analysis

as_igraph(): Convert Atlas Connectivity to igraph
atlas_connectivity(): Compute Connectivity Matrix from Atlas Parcellations
atlas_graph(): Compute Parcel Adjacency Graph from an Atlas
atlas_hierarchy(): Atlas Hierarchy
atlas_overlap(): Cross-Atlas Overlap Analysis
dilate_atlas(): Dilate Atlas Parcellation Boundaries
query_point(): Look Up Atlas Regions at MNI Coordinates
spin_test(): Spin Test for Spatial Correlation Significance

Supporting methods

plot(<atlas>) plot(<glasser>) plot(<surfatlas>): Plot Glasser Atlas
print(<atlas>) print(<atlas_provenance>) print(<glasser>) print(<schaefer>): Print Methods for neuroatlas Objects
print(<atlas_alignment>): Print Method for Atlas Alignment Results
print(<atlas_ref>): Print Method for Atlas References
print(<atlas_spec>): Print an atlas_spec
print(<atlas_transform_plan>): Print Method for Transform Plans
print(<templateflow>): Print a TemplateFlow Object