Atlases — DKT is default, not exclusive

DLSurfer produces a FreeSurfer-shaped subject tree. Which cortical atlas is labeled is a profile/engine choice. DKT is the default because FastSurferVINN / common DWI handoffs use it — not because DLSurfer is a “DKT-only” tool.

Supported atlas surface

Atlas	Status in DLSurfer	FreeSurfer	FastSurfer	How
DKT (DKTatlas)	Default (core)	Yes	Native	--atlas dkt (default)
Desikan–Killiany (DK)	Wired	Yes	--fsaparc	--atlas dk or profile core-dk
Destrieux (a2009s)	Wired	Yes	After sphere.reg	profile atlas-destrieux
Schaefer	Wired	Project	Project	profile atlas-schaefer (SCHAEFER_ANNOT_*)
HCP-MMP / Yeo	Same pattern as Schaefer	Project	Project	Documented runner-up; reuse surf2surf
aseg	Always with core	Yes	Yes	Not a cortical choice

Design rules

1. Default profile stays DKT for FastSurferVINN parity.
2. Atlas is a parameter, not a fork of the package.
3. Do not bake DKT connectome node tables into DLSurfer. Node lists / LUT / disconnectome live in the connectome pipeline.
4. Multiple atlases can coexist in one SUBJECTS_DIR as additional .annot / stats files (FreeSurfer pattern).

CLI

dlsurfer atlases
dlsurfer run --profile core --atlas dkt
dlsurfer run --profile core --atlas dk          # FastSurfer --fsaparc
dlsurfer run --profile core-dk                  # same intent
dlsurfer run --profile atlas-destrieux --t1 …   # needs existing surfaces
dlsurfer run --profile atlas-schaefer --t1 …