Reduce a subcortical atlas to focus regions on grey anatomical context

Applies the post-processing recipe shared by the FreeSurfer subcortical atlases:

Usage

aseg_context(
  atlas,
  focus,
  match_on = c("label", "region"),
  remove = aseg_hidden_labels(),
  punch_white_matter = TRUE,
  cortex = "^cortex",
  white_matter = "White-Matter$",
  drop_empty_views = TRUE
)

Arguments

atlas

A subcortical ggseg_atlas, e.g. from create_subcortical_from_volume().

focus

Regex matched (case-insensitively) against match_on identifying the regions to keep as coloured core; everything else becomes context.

match_on

Column to match focus against: "label" or "region".

remove

Character vector of ggseg.formats::atlas_region_remove() patterns to strip before demoting context. Defaults to aseg_hidden_labels(); pass character(0) to skip.

punch_white_matter

If TRUE, subtract white_matter from the cortex silhouette. Skipped with a message if either pattern is absent.

cortex, white_matter

Label patterns for the brain silhouette and the cerebral white matter used by the punch.

drop_empty_views

If TRUE, remove views containing no focus region.

Value

The post-processed ggseg_atlas.

Details

1. Punch the cerebral white matter out of the brain silhouette (ggseg.formats::atlas_region_op()) so slices show the cortical ribbon with the white-matter interior as a hole rather than a solid blob.

2. Remove the structures aseg does not draw (aseg_hidden_labels()).

3. Demote every remaining structure that is not matched by focus to grey context, so only the focus regions are coloured.

4. Optionally drop views left with no focus geometry.

The context demotion matches the leftover core labels exactly and case-sensitively, so a focus region is never swallowed by a context entry that happens to be a substring of its name (e.g. Thalamus vs hypothalamus).

See also

subcortical_views(), ggseg.formats::atlas_region_contextual()

Examples

if (FALSE) { # \dontrun{
atlas <- create_subcortical_from_volume(
  input_volume = file.path(
    freesurfer::fs_subj_dir(), "fsaverage5", "mri", "aseg.mgz"
  ),
  atlas_name = "aseg"
)
aseg_context(atlas, focus = "Hippocampus")
} # }