Converting legacy atlases • ggseg.extra

If you have atlases from older versions of ggseg or ggseg3d, this vignette explains how to convert them to the current ggseg_atlas format.

library(ggseg.formats)
library(ggseg)
library(ggseg3d)

The old system

Previous versions used separate objects for 2D and 3D rendering:

ggseg_atlas objects for 2D plots with ggseg()
ggseg3d_atlas objects for 3D plots with ggseg3d()

Atlas packages exported pairs like dk and dk_3d, or yeo7 and yeo7_3d. You had to remember which object to use with which package.

The current system

The current system uses a single ggseg_atlas object that works with both packages. One atlas, both renderers.

Converting old atlases

Use convert_legacy_brain_atlas() to convert old atlas objects:

From a ggseg3d_atlas only

unified <- convert_legacy_brain_atlas(atlas_3d = old_atlas_3d)

ggseg3d(atlas = unified)

From both 2D and 3D objects

unified <- convert_legacy_brain_atlas(
  atlas_2d = old_atlas,
  atlas_3d = old_atlas_3d
)

ggplot() + geom_brain(atlas = unified)

ggseg3d(atlas = unified)

From a 2D ggseg_atlas only

unified <- convert_legacy_brain_atlas(atlas_2d = old_atlas)

ggplot() + geom_brain(atlas = unified)

This atlas works with ggseg but not ggseg3d (no 3D vertex data).

Specifying atlas type

The function auto-detects atlas type from the structure. Override if needed:

unified <- convert_legacy_brain_atlas(
  atlas_2d = old_atlas,
  atlas_3d = old_atlas_3d,
  atlas_name = "my_atlas",
  type = "cortical"
)

Valid types: “cortical”, “subcortical”, “tract”.

Batch conversion

When converting many atlas packages, load the .rda files into isolated environments to avoid name collisions:

env <- new.env()
load("data/my_atlas.rda", envir = env)
atlas_2d <- env[["my_atlas"]]

result <- convert_legacy_brain_atlas(atlas_2d = atlas_2d)

save(my_atlas = result, file = "data/my_atlas.rda", compress = "xz")

Always save with compress = "xz" for significant file size reduction.

Post-conversion checklist

After converting, verify the result:

stopifnot(is_ggseg_atlas(result))

nrow(result$core)
length(result$palette)

Each converted atlas package needs these updates:

DESCRIPTION: Add ggseg.formats to Depends, remove ggseg/ggseg3d from Depends
R/data.R: Update roxygen2 docs to reference ggseg_atlas format
R/-package.R: Add @import ggseg.formats
tests: Use is_ggseg_atlas() and geom_brain() instead of legacy is_ggseg_atlas() and ggseg()
R/sysdata.rda: Delete. Palettes are embedded in the atlas object (atlas$palette), not stored separately in brain_pals

Lessons learned from batch conversion

The ggseg ecosystem converted 19 atlas packages using this function. Key findings:

3D data is not always preserved

Subcortical atlases that only had 3D mesh data (no 2D sf geometry) lose their meshes during conversion. The converter cannot round-trip standalone meshes back into the new format. These atlases need recreation from source FreeSurfer files using create_subcortical_from_volume().

Cortical 3D atlases fare better — vertex indices can be inferred from mesh coordinates — but the result is still approximate. Recreation produces more accurate vertex mappings.

Palette entries may not match core rows exactly

Some converted atlases have palette entries for labels absent from core (e.g., "lh_unknown", "rh_???", or labels with special characters). This is normal: the palette retains all labels from the original annotation, while core only contains labels that have geometry. is_ggseg_atlas() emits an informational message but still validates.

Labels with special characters lose sf coverage

Atlases like Brainnetome have labels containing slashes (e.g., "A9/46d_L"). These labels may exist in core but have no matching polygon geometry, reducing sf coverage below 100%. This is a data issue in the source atlas, not a conversion bug.

Skip ggseg3d tests for atlases without 3D data

If a converted atlas has no vertices or meshes, ggseg3d() will error. Either omit the 3D test entirely or guard it:

it("renders with ggseg3d", {
  skip_if_not_installed("ggseg3d")
  skip_if(is.null(my_atlas$geometry$vertices), "No 3D data")
  p <- ggseg3d::ggseg3d(atlas = my_atlas)
  expect_s3_class(p, "htmlwidget")
})

Troubleshooting

No vertices inferred: The mesh coordinates don’t align with the brain surface. Check that surface matches what was used to create the 3D atlas.

Wrong hemisphere assignment: The function infers hemisphere from the hemi column. If this is missing or wrong, set it manually after conversion.

Type detection fails: Set type explicitly.

When to recreate instead

Converting works for getting legacy atlases running with ggseg 2.0, but recreating from source data produces better results. Use the creation functions if you have access to the original neuroimaging files:

create_cortical_from_annotation() — from FreeSurfer annotation files
create_subcortical_from_volume() — from volumetric segmentation
create_tract_from_tractography() — from tractography files
create_cortical_from_labels() — from individual label files

See the cortical, subcortical, tract, and label-based atlas tutorials.