Package: neuroatlas 0.1.0.9000

neuroatlas: Neuroimaging Atlases and Parcellations

Provides a unified interface to access and work with various neuroimaging atlases and parcellations including Schaefer, Brainnetome, Glasser, FreeSurfer ASEG, and Olsen MTL atlases. Integrates with TemplateFlow for standardized template access and supports interactive brain surface visualisation via triangle-mesh rendering with 'ggplot2' and 'ggiraph'.

Authors:Bradley Buchsbaum [aut, cre]

neuroatlas_0.1.0.9000.tar.gz
neuroatlas_0.1.0.9000.zip(r-4.7)neuroatlas_0.1.0.9000.zip(r-4.6)neuroatlas_0.1.0.9000.zip(r-4.5)
neuroatlas_0.1.0.9000.tgz(r-4.6-any)neuroatlas_0.1.0.9000.tgz(r-4.5-any)
neuroatlas_0.1.0.9000.tar.gz(r-4.7-any)neuroatlas_0.1.0.9000.tar.gz(r-4.6-any)
neuroatlas_0.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
neuroatlas/json (API)

# Install 'neuroatlas' in R:
install.packages('neuroatlas', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bbuchsbaum/neuroatlas/issues

Pkgdown/docs site:https://bbuchsbaum.github.io

Datasets:
  • fsaverage - Surface geometry for the fsaverage6 atlas
  • olsen_mtl - Olsen Medial Temporal Lobe Atlas

On CRAN:

Conda:

atlasneuroimagingparcellation

3.80 score 3 stars 15 scripts 136 exports 128 dependencies

Last updated from:7d1d7929fe. Checks:4 WARNING, 2 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING423
source / vignettesOK418
linux-release-x86_64WARNING375
macos-release-arm64WARNING212
macos-oldrel-arm64WARNING316
windows-develERROR372
windows-releaseERROR369
windows-oldrelERROR338
wasm-releaseOK308

Exports:%where%as_igraphas_parcel_dataatlas_alignmentatlas_artifactsatlas_connectivityatlas_coord_spaceatlas_familyatlas_graphatlas_hierarchyatlas_historyatlas_overlapatlas_provenanceatlas_refatlas_roi_colorsatlas_spaceatlas_transform_manifestatlas_transform_planbatch_reducebrainnetome_labelsbuild_brain_polygon_databuild_cluster_explorer_databuild_conflict_edgesbuild_surface_polygon_datacheck_templateflowclear_templateflow_cachecluster_explorercoord_spacescreate_templateflowdilate_atlasfilter_atlasget_aseg_atlasget_atlasget_brainnetome_atlasget_fsl_atlasget_ggseg_atlasget_glasser_atlasget_harvard_oxford_atlasget_harvard_oxford_cortical_atlasget_harvard_oxford_cortical_subcortical_atlasget_harvard_oxford_subcortical_atlasget_hipp_atlasget_julich_brain_atlasget_olsen_mtlget_roiget_schaefer_atlasget_schaefer_surfatlasget_space_transformget_subcortical_atlasget_surface_coordinate_spaceget_surface_templateget_templateget_template_brainmaskget_template_csfget_template_gmget_template_headget_template_legacyget_template_probsegget_template_schaeferget_template_wmget_visfatlasget_visual_atlasget_wang_atlasget_wang_prob_atlasggseg_schaeferglasser_surfinfer_design_var_typeinstall_templateflowlaunch_cluster_explorerlist_atlasesload_surface_templatemap_atlasmap_to_schaefermerge_atlasesMNI152_to_MNI305MNI305_to_MNI152needs_coord_transformneeds_template_warpneeds_transformnetwork_anchor_huesnew_atlas_refparcel_dataparcel_valuesplot_brainplot_brain_gridplot_glasserproject_surface_viewquery_coordquery_pointquery_voxread_parcel_datareduce_atlasreduce_atlas_vecresampleroi_attributesroi_colors_embeddingroi_colors_maximin_viewroi_colors_network_harmonyroi_colors_rule_hclroi_metadataschaefer_surfschaefer_surf_optionsshow_templateflow_cache_pathspace_transform_manifestspin_testsub_atlassubcortical_atlas_optionssy_100_17sy_100_7sy_1000_17sy_1000_7sy_200_17sy_200_7sy_300_17sy_300_7sy_400_17sy_400_7sy_500_17sy_500_7sy_600_17sy_600_7sy_700_17sy_700_7sy_800_17sy_800_7sy_900_17sy_900_7template_to_coord_spacetemplatestflow_filestflow_spacestransform_coordstransform_vertices_to_volumevalidate_atlas_refvalidate_parcel_datawrite_parcel_data

Dependencies:askpassassertthatbase64encbigassertrbigparallelrbigstatsrbitbit64bitopsbslibcachemcaToolsclicliprcodetoolscolorplanecowplotcpp11crayoncurldbscandeflistdigestdoParalleldownloaderdplyrevaluatefarverfastmapffflockFNNfontawesomefontBitstreamVerafontLiberationfontquiverforeachfsfuturefuture.applygdtoolsgenericsggiraphggplot2giftiglobalsgluegplotsgtablegtoolshighrhmshtmltoolshtmlwidgetshttr2igraphisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelistenvmagrittrMASSMatrixmemoisemimemmapneuroim2neurosurfopensslparallellypatchworkpillarpkgconfigplyrpngprettyunitsprogresspspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadrrglRhpcBLASctlrlangrmarkdownrmioRnanoflannRNiftiRNiftyRegroptimRSpectraRvcgS7sassscalesscicostringistringrsyssystemfontstemplateflowtibbletidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Filter Atlas with Infix Operator%where%
Convert Atlas Connectivity to igraphas_igraph as_igraph.atlas_connectivity
Convert an Object to `parcel_data`as_parcel_data as_parcel_data.atlas as_parcel_data.default as_parcel_data.parcel_data
Atlas Alignment Lookupatlas_alignment
Get Atlas Artifact Metadataatlas_artifacts
Compute Connectivity Matrix from Atlas Parcellationsatlas_connectivity
Atlas Coordinate-Space Convenience Accessoratlas_coord_space
Atlas Family Convenience Accessoratlas_family
Compute Parcel Adjacency Graph from an Atlasatlas_graph
Atlas Hierarchyatlas_hierarchy
Get Atlas Processing Historyatlas_history
Cross-Atlas Overlap Analysisatlas_overlap
Atlas Provenance Accessorsatlas_artifacts.atlas atlas_artifacts.default atlas_history.atlas atlas_history.default atlas_provenance atlas_provenance.atlas atlas_provenance.default
Atlas Reference Accessoratlas_ref atlas_ref.atlas atlas_ref.default
Assign optimal colours to atlas regionsatlas_roi_colors
Atlas Template-Space Convenience Accessoratlas_space
Atlas Transform Manifestatlas_transform_manifest
Plan a Transform Between Spacesatlas_transform_plan
Batch Reduce Multiple Volumes by an Atlasbatch_reduce
Brainnetome Atlas Label Tablebrainnetome_labels
Build brain polygon render data for a surface atlasbuild_brain_polygon_data
Build Cluster Explorer Databuild_cluster_explorer_data
Build slice-aware conflict edges between ROIsbuild_conflict_edges
Build Surface Polygon Data for Renderingbuild_surface_polygon_data
Check TemplateFlow Installation Statuscheck_templateflow
Clear neuroatlas TemplateFlow Cacheclear_templateflow_cache
Launch Cluster Explorer Shiny Appcluster_explorer
Standard Coordinate Space Identifierscoord_spaces
Coordinate Space Transforms for Neuroimaging Templatescoordinate_spaces
Create a TemplateFlow Interface Objectcreate_templateflow
Dilate Atlas Parcellation Boundariesdilate_atlas
Filter Atlas by ROI Attributesfilter_atlas filter_atlas.atlas
Surface geometry for the fsaverage6 atlasfsaverage
Get the FreeSurfer Subcortical Atlas (ASEG)get_aseg_atlas
Load an Atlas by Registered IDget_atlas
Load Brainnetome 246-Region Atlasget_brainnetome_atlas
FSL Atlas Loadersget_fsl_atlas
Get ggseg-Compatible Schaefer Atlasget_ggseg_atlas
Load Glasser Atlasget_glasser_atlas
Load a Harvard-Oxford Atlasget_harvard_oxford_atlas get_harvard_oxford_cortical_atlas get_harvard_oxford_cortical_subcortical_atlas get_harvard_oxford_subcortical_atlas
Extract Hippocampal Parcellationget_hipp_atlas
Load a Julich-Brain FSL Atlasget_julich_brain_atlas
Load Olsen MTL Atlasget_olsen_mtl
Extract a region of interest (ROI) from an atlasget_roi get_roi.atlas
Extract regions of interest from a surface atlasget_roi.surfatlas
Load Schaefer Brain Parcellation Atlasget_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
Load Surface-Based Schaefer Atlasget_schaefer_surfatlas
Get Transform Matrix Between Coordinate Spacesget_space_transform
Load harmonized subcortical atlases via TemplateFlowget_subcortical_atlas
Get Coordinate Space for a Surface Templateget_surface_coordinate_space
Fetch a Template from TemplateFlowget_surface_template get_template
visfAtlas Probabilistic Functional Visual Atlas (volume)get_visfatlas
Early Visual Cortex Atlas (V1-V5, cytoarchitectonic)get_visual_atlas
Wang (2015) Probabilistic Visual Topography Atlasget_wang_atlas
Wang (2015) Full Per-Area Probability Volumes (Princeton ProbAtlas_v4)get_wang_prob_atlas print.wang_prob_paths
Create Interactive Schaefer Atlas Visualizationggseg_schaefer
Glasser Surface Atlas (fsaverage)glasser_surf
Infer Design Variable Typeinfer_design_var_type
Install Templateflow (DEPRECATED)install_templateflow
Launch Cluster Explorer in Interactive Sessionlaunch_cluster_explorer
List Registered Atlaseslist_atlases
Load a surface template as a neurosurf geometryload_surface_template
Map values to an atlasmap_atlas map_atlas.atlas map_atlas.glasser map_atlas.schaefer
Map Values to Schaefer Atlas Formatmap_to_schaefer
Merge Two Brain Atlasesmerge_atlases
MNI152 to MNI305 Affine Transform MatrixMNI152_to_MNI305
MNI305 to MNI152 Affine Transform MatrixMNI305_to_MNI152
Check if a Coordinate Transform is Neededneeds_coord_transform
Check if a Nonlinear Template Warp is Neededneeds_template_warp
Check if Transform is Needed Between Spacesneeds_transform
Assign harmonic anchor hues to networksnetwork_anchor_hues
Atlas Reference Metadatanew_atlas_ref
Olsen Medial Temporal Lobe Atlasolsen_mtl
Parcel-Level Data Containerparcel_data
Extract Parcel Values Aligned to an Atlasparcel_values
Plot Brain Surface Atlasplot_brain
Multi-panel Brain Plot Gridplot_brain_grid
Plot Glasser Atlas Valuesplot_glasser
Plot Glasser Atlasplot-methods plot.atlas plot.glasser plot.surfatlas
Print Methods for neuroatlas Objectsprint-methods print.atlas print.atlas_provenance print.glasser print.schaefer
Print Method for Atlas Alignment Resultsprint.atlas_alignment
Print Method for Atlas Referencesprint.atlas_ref
Print Method for Transform Plansprint.atlas_transform_plan
Print a TemplateFlow Objectprint.templateflow
Project Surface Vertices to a Canonical 2D Viewproject_surface_view
Query Atlas Labels by Coordinatequery_coord query_vox
Look Up Atlas Regions at MNI Coordinatesquery_point
Read a `parcel_data` Object from Diskread_parcel_data
Reduce a NeuroVol or NeuroVec by an Atlasreduce_atlas reduce_atlas.atlas
Reduce a NeuroVec by an Atlas to a ClusteredNeuroVecreduce_atlas_vec reduce_atlas_vec.atlas
Resample Volume to New Spaceresample
List Available ROI Attributesroi_attributes roi_attributes.atlas
Embedding-based palette with smooth gradientsroi_colors_embedding
Slice-aware maximin palette for ROIsroi_colors_maximin_view
Network-harmonic palette with neighbour separationroi_colors_network_harmony
Deterministic HCL palette with harmonic variationroi_colors_rule_hcl
ROI Metadata Functionsroi_metadata roi_metadata.atlas
Schaefer Surface Atlasschaefer_surf
List supported Schaefer surface atlas variantsschaefer_surf_options
Show neuroatlas TemplateFlow Cache Pathshow_templateflow_cache_path
Space Transform Manifestspace_transform_manifest
Spin Test for Spatial Correlation Significancespin_test
Select a Subset of Atlas Regionssub_atlas sub_atlas.atlas sub_atlas.surfatlas
Subcortical Atlas Options (TemplateFlow-backed)subcortical_atlas_options
Get Coordinate Space for Any Templatetemplate_to_coord_space
Find TemplateFlow Files Matching Metadata Criteriatflow_files
List Available TemplateFlow Template Spacestflow_spaces
Transform Coordinates Between Spacestransform_coords
Transform Surface Vertices to Volume Spacetransform_vertices_to_volume
Validate an Atlas Referencevalidate_atlas_ref
Validate a Parcel-Level Data Objectvalidate_parcel_data
Write a `parcel_data` Object to Diskwrite_parcel_data