What DLSurfer does¶
One paragraph per stage (same spirit as DKT Connectome’s step pages).
| Stage | What happens | Default engine |
|---|---|---|
| Fill (optional) | Inpaint lesion cavity on T1w so VINN/surfaces see contiguous anatomy | neuroLIT standalone (core-lesion) |
| Segment | Whole-brain DKT/aseg (+ CC, CerebNet, HypVINN) | FastSurfer VINN --seg_only --tal_reg |
| Surfaces | White/pial, sphere, thickness, aparc in SUBJECTS_DIR | recon-surf --surf_only |
| Post (optional) | Pack LIT products into the FS tree | lit-postprocessing |
| Specialty | Claustrum, HA/BS/thal, SynthSR, TopoFit, … | Profile-selected |
Biological note (lesions): Large lesions break cortical surface reconstruction because FastSurfer/FreeSurfer expect contiguous GM. Fill modifies T1w before segmentation/surfaces so labels can be estimated on a plausible whole-brain anatomy. That is not a claim that tissue inside the lesion is healthy.
Not DWI / not DKT connectome: Tractography, SIFT2, disconnectome, and QSIPrep live in DKT Connectome. DLSurfer only owns T1 morphometry orchestration; see Isolation.
Engine policy: Wrap FastSurfer/FS for production SUBJECTS_DIR — why.