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Load harmonized subcortical atlases via TemplateFlow

Source: R/subcortical_atlases.R
get_subcortical_atlas.Rd

Fetches one of the AtlasPack-derived subcortical atlases (CIT168, HCP thalamus, MDTB10 cerebellum, or HCP hippocampus/amygdala) using the existing TemplateFlow integration. The returned object includes the source template space and resolution so downstream workflows can track provenance.

Usage

get_subcortical_atlas(
  name,
  template_space = NULL,
  resolution = NULL,
  desc = NULL,
  outspace = NULL,
  use_cache = TRUE,
  path_only = FALSE,
  ...
)

Arguments

name

Atlas identifier; see subcortical_atlas_options(). Aliases such as "thalamus_hcp" or "cerebellum" are accepted.

template_space

TemplateFlow space to download (e.g., "MNI152NLin6Asym" or "MNI152NLin2009cAsym"). Defaults to the atlas-specific recommended space.

resolution

TemplateFlow resolution (e.g., "01"). Defaults to the atlas recommendation; validated against known options for the atlas.

desc

Optional TemplateFlow desc to override the atlas default (e.g., "LRSplit" for CIT168 hemispheric split).

outspace

Optional NeuroSpace or TemplateFlow query (string/list) to resample the atlas into a different space.

use_cache

Logical; pass through to get_template.

path_only

Logical; if TRUE, return paths to the atlas/label files plus metadata instead of loading into R objects.

...

Additional arguments forwarded to get_template.

Value

When path_only=FALSE (default), a list with classes c("subcortical", "atlas") containing:

  • name: human-friendly atlas name

  • atlas: ClusteredNeuroVol with parcellation labels

  • ids: integer vector of region IDs

  • labels: character vector of region labels

  • orig_labels: same as labels

  • hemi: inferred hemisphere labels when available

  • cmap: optional RGB mapping if provided by the label file

  • space, resolution, desc: TemplateFlow metadata

  • template_atlas: TemplateFlow atlas parameter used

When path_only=TRUE, a list with class c("subcortical_paths","list") containing atlas_path, label_path, and the same metadata fields above.

Examples

if (FALSE) { # \dontrun{
# Load CIT168 in NLin6Asym space
cit <- get_subcortical_atlas("cit168", template_space = "MNI152NLin6Asym")

# Get only the file paths without loading volumes
paths <- get_subcortical_atlas("mdtb10", path_only = TRUE)
} # }