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Create cortical atlas from a neuromaps annotation

Source: R/atlas_cortical.R
create_cortical_from_neuromaps.Rd

[Experimental]

Build a brain atlas directly from a neuromaps annotation. The annotation is downloaded via neuromapr::fetch_neuromaps_annotation().

Supports both surface (.func.gii) and volume (.nii/.nii.gz) annotations. Volume annotations in MNI152 space are automatically projected to fsaverage5 via FreeSurfer's mri_vol2surf.

Usage

create_cortical_from_neuromaps(
  source,
  desc,
  space = "fsaverage",
  density = "10k",
  label_table = NULL,
  n_bins = NULL,
  atlas_name = NULL,
  output_dir = NULL,
  hemisphere = c("rh", "lh"),
  views = c("lateral", "medial", "superior", "inferior"),
  tolerance = NULL,
  smooth_refinements = NULL,
  cleanup = NULL,
  verbose = get_verbose(),
  skip_existing = NULL
)

Arguments

source

Neuromaps source identifier (e.g., "schaefer").

desc

Neuromaps descriptor key (e.g., "400Parcels7Networks").

space

Coordinate space. Defaults to "fsaverage".

density

Surface vertex density. Defaults to "10k".

label_table

Optional data.frame mapping parcel IDs to region names.

n_bins

Number of quantile bins for continuous brain maps.

atlas_name

Name for the atlas. If NULL, derived from the input filename.

output_dir

Directory to store intermediate files (screenshots, masks, contours). Defaults to tempdir().

hemisphere

Which hemispheres to include: "lh", "rh", or both.

views

Which views to include: "lateral", "medial", "superior", "inferior".

tolerance

[Deprecated] sf simplification is no longer applied during atlas creation. Use atlas_smooth() on the returned atlas instead. Supplying a value emits a lifecycle warning and is otherwise ignored.

smooth_refinements

[Deprecated] sf-side smoothing is no longer applied during atlas creation. Use atlas_smooth() on the returned atlas instead. Supplying a value emits a lifecycle warning and is otherwise ignored.

cleanup

Remove intermediate files after atlas creation. If not specified, uses options("ggseg.extra.cleanup") or the GGSEG_EXTRA_CLEANUP environment variable. Default is TRUE.

verbose

Verbosity level: 0 (silent), 1 (standard progress, default), or 2 (debug, includes FreeSurfer output). Logical values are accepted (TRUE = 1, FALSE = 0). If not specified, uses the value from options("ggseg.extra.verbose") or the GGSEG_EXTRA_VERBOSE environment variable.

skip_existing

Skip generating output files that already exist, allowing interrupted atlas creation to resume. If not specified, uses options("ggseg.extra.skip_existing") or the GGSEG_EXTRA_SKIP_EXISTING environment variable. Default is TRUE.

Value

A ggseg_atlas object.

Examples

if (FALSE) { # \dontrun{
atlas <- create_cortical_from_neuromaps(
  source = "abagen",
  desc = "genepc1",
  n_bins = 7
)
} # }