NEWS

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ggseg.extra 2.0.1

Cortical pipeline: mesh projection

The cortical atlas pipeline now projects inflated mesh triangles directly to 2D polygons via orthographic projection, replacing the screenshot-based contour extraction from v2.0.0.

• Much faster — atlas creation completes in ~5 seconds instead of minutes.
• Cleaner geometry — no pixel staircase artifacts from rasterisation.
• Fewer dependencies — no FreeSurfer rendering, ImageMagick, or Chrome needed for 2D geometry (FreeSurfer is still required to read annotation files).
• Better small-region visibility — boundary faces are assigned to the smallest neighbouring region so tiny parcels are not swallowed by their neighbours.
• Smooth region borders — boundary triangles (vertices in different regions) are split along edge midpoints so each region gets a clean polygon slice, eliminating the sawtooth artifacts from whole-triangle assignment.

Breaking changes

• Removed method, snapshot_dim, smoothness, and steps parameters from all create_cortical_from_*() functions. The pipeline always reads data and projects to 2D in one pass — no step-based control needed.
• Changed default tolerance from 0.5 to 1 — the triangle-splitting approach produces smoother borders that tolerate higher simplification.

Lighter dependency footprint

• Moved chromote, htmlwidgets, magick, smoothr, terra, RNifti, and freesurfer from Imports to Suggests. Users who only need the cortical pipeline no longer need these packages installed. They are checked at runtime and requested when needed (subcortical, tract, and volumetric pipelines).

New internals

• Added R/mesh-projection.R with the full geometric projection algorithm: orthonormal view basis computation, backface culling, per-face label assignment, and triangle-to-polygon union via sf.

ggseg.extra 2.0.0

• Major rewrite of atlas creation pipelines with modular step-based architecture
• Added GIFTI (.label.gii) and CIFTI (.dlabel.nii) annotation support
• Added neuromaps surface and volume annotation pipelines
• Added whole-brain atlas creation from volumetric parcellations
• Added white-matter tract atlas creation from tractography files
• Added three-level verbosity control (silent/standard/debug)
• Deprecated ggseg_atlas_repos(), install_ggseg_atlas(), and install_ggseg_atlas_all() in favour of 'ggseg.hub'
• Moved convert_legacy_brain_atlas() to 'ggseg.formats' (re-exported)
• Removed rgdal, purrr, reticulate, and tidyr dependencies
• Replaced reticulate/kaleido snapshots with chromote
• Protected all parallel operations against multicore fork crashes
• Removed dead FreeSurfer wrapper functions
• Fixed read_ctab for multi-word labels
• Fixed subcortical label classification in whole-brain pipeline

ggseg.extra 1.9.9.9001

Boundary triangle splitting

Boundary triangles (where vertices belong to different atlas regions) are now split into sub-polygons along edge midpoints instead of being assigned wholesale to a single region. This eliminates the sawtooth artifacts at region borders that resulted from the triangular mesh geometry.

• 2-region boundaries: triangle is split at the midpoints of the two cross-boundary edges — the majority region gets a quadrilateral, the minority region gets a triangle.
• 3-region boundaries: triangle is divided into three quadrilaterals meeting at the centroid.
• Default tolerance increased from 0.5 to 1 — the smoother borders tolerate higher simplification without visible degradation.

Bug fixes

• ensure_fs_compatible_nifti() no longer errors when the NIfTI header cannot be read (e.g. .mgz files or nonexistent paths). It now falls through gracefully and lets downstream FreeSurfer commands handle the file.

ggseg.extra 1.6

1.6.0

• Removed rgdal dependency, replaced with sf/terra (#49, #59)
• Fixed r-universe API calls (JSON array format change)
• Fixed vignette build issues with conditional evaluation for suggested packages
• Replaced reticulate/kaleido with webshot2 for plotly screenshots
• Updated system setup vignette with new requirements
• Added documentation for parallel processing and progress bars
• Added note about freesurfer dev version requirement
• Updated CITATION to use bibentry()
• Updated pkgdown site with ggseg brand styling
• Fixed mris_label2annot example documentation

ggseg.extra 1.5

1.5.33.003

• small bug fix that prevented calls to FreeSurfer
• Possibility to initiate new atlas project from the RStudio Project GUI

ggseg.extra 1.5.33

• removes purrr dependency
• used ggseg r-universe as install repo for install functions

ggseg.extra 1.5.32

• non-standard columns in 3d atlas are retained in 2d atlas
• Freesurfer annotation file custom S3 class implemented
• progressbar for region snapshots

ggseg.extra 1.5.3

• Added pipeline functions for:
  • creating ggseg3d-atlas from annotation files
  • creating ggseg3d-atlas from volumetric files
  • creating ggseg-atlas from cortical ggseg3d-atlas
  • creating ggseg-atlas from volumetric files
• Added a NEWS.md file to track changes to the package.