DLSurfer phases — status
| Phase |
Goal |
Status in v0.1 |
| 0 Spec freeze |
Claims, pins, engine choices, XOR engines |
Done — docs/CLAIMS.md, engines.yaml, profiles.yaml |
| 1 MVP |
CLI, doctor, core / core-lesion, dry-run plans, HPC template |
Done — dlsurfer package |
| 2 FS8 + handoff |
fs8, utilities (EasyReg/SynthMorph/DeepN4), DKT handoff cmd |
Done — profiles + dlsurfer handoff-dkt |
| 3 surf-dl |
TopoFit, V2C-Flow, SUGAR, thickness-fast (experimental) |
In progress — TopoFit ±LIT GPU job; V2C/SUGAR/CTE still open |
| 4 Harden / metrics |
metrics TSV on --execute, citation boilerplate, publish notes |
Done — runner summary + docs/PUBLISH.md / LIVE_RUNS.md |
| 5 Live ops |
Cluster bind, EG smoke, specialty gates |
Partial — container env READY; core_lesion_eg_smoke passed; TBI±LIT baseline report; Phase-3 CSR still open |
Best-ready choices (locked in engines.yaml)
| Stage |
Chosen |
Why (short) |
| Skull-strip |
SynthStrip |
Production in FS |
| Bias (optional) |
DeepN4 |
Best Ready N4 approx |
| Whole-brain seg |
FastSurferVINN |
Production default; SynthSeg for odd contrast |
| CC / cereb / hypothal |
FastSurfer modules |
Production parity |
| Lesion |
neuroLIT standalone |
Production; keeps GPU/CPU split |
| Surfaces (default) |
recon-surf |
Classical but Production FS contract |
| Surfaces (Phase 3) |
TopoFit → V2C-Flow |
Production WM / Ready full CSR |
| Volume reg utils |
EasyReg + SynthMorph |
Production in FS |
| sphere.reg (Phase 3) |
SUGAR |
Ready dedicated spherical reg |
| Thickness-only |
DL-CTE family |
Ready; not for connectome |
| Alt engine |
FreeSurfer 8 |
Production XOR |
Still required for “live” Phase 5 / science gates
See LIVE_RUNS.md and dlsurfer gates.
- Install / bind FastSurfer 2.6 + neuroLIT + FS8 on the cluster →
dlsurfer doctor READY.
- EG smoke:
dlsurfer run --profile core-lesion … --execute → mark core_lesion_eg_smoke passed.
- TBI±LIT gate →
tbi_lit_surfaces passed before promoting surf-dl-*.
- SynthSeg-PC vs JLF →
synthseg_pc_vs_jlf passed before IDEAS PC production.
- Cohort timing vs legacy multi-job (
dlsurfer_metrics.tsv + SLURM queue).