wwu-mmll / confound_corrected_cpm / 28577330990

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push

github

Committed by NilsWinter

Commit Message

Add built-in atlas registry with 15 bundled MNI coordinate sets

Users can now select an atlas by name (e.g. atlas="Schaefer100-17") instead
of hand-building a coordinate CSV. A single `atlas` parameter accepts either a
built-in name or a path to a custom CSV; the old `atlas_labels` parameter is
deprecated (still works, `atlas` wins if both given) and slated for removal.

- New cccpm.atlases package: resolve_atlas / load_atlas / list_atlases, with a
  path-vs-name resolver and required-column validation.
- 15 bundled coordinate tables (region,x,y,z[,network],hemisphere,structure)
  regenerated from authentic public sources by scripts/generate_atlas_data.py
  (provenance in data/SOURCES.md): Schaefer 100-400 x7/x17, Power264,
  Dosenbach160, Seitzman300, Destrieux148, HarvardOxfordCortical, AAL116,
  Glasser360. Surface atlases use published volumetric-MNI versions with
  computed centroids.
- CPMAnalysis: node-count validation against the connectome dimension; resolved
  atlas saved to results for a self-contained report. Network-summary + chord
  auto-enable when the atlas carries a `network` column.
- Quickstarts updated to a 100-node sim using atlas="Schaefer100-17".
- Tests for registry, resolution, deprecation, and node-count guard.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

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