Live runs — ops checklist¶

1. Bind tools¶

cd …/preprocessing/DL/dlsurfer
source env/cluster_containers.sh
PYTHONPATH=. python -m dlsurfer doctor   # [READY]

Exports SIFs, SCHAEFER_ANNOT_{LH,RH}, V2C_ROOT, SYNTHSEG_PC_*.
Optional meta-image: containers/dlsurfer.def + entrypoint_bids.sh.

2. EG smoke — passed (incl. GPU confirmatory)¶

Arm	Status
Standalone FS2.6+LIT science	Done (prior)
GPU job 191960	COMPLETED — `work/eg_gpu_core_lesion/sub-EG/scripts/recon-surf.done`
Metrics vs sacct	`work/eg_gpu_core_lesion/metrics_vs_slurm.json` (~6991s compute / 01:56:33 wall)

3. Gates¶

Gate	Choice (literature)	Status
`tbi_lit_topofit`	TopoFit (FS-shipped WM)	passed + Chamfer QC / FreeView script
`tbi_lit_surfaces`	V2C-Flow (best Ready full CSR)	open — clone + `dlsurfer-v2c`; need `vox2organ` env
`tbi_lit_sphere_sugar`	SUGAR	open — set `SUGAR_ROOT`
`tbi_lit_thickness`	DL-CTE family	open — set `DL_CTE_ROOT`
`synthseg_pc_vs_jlf`	JLF production until PC ≥ JLF	open — env wired; Hammers val dirs
`core_lesion_eg_smoke`	—	passed

sbatch hpc/sbatch_phase3_v2c_tbi_lit.sh   # after conda env vox2organ
bash scripts/eval_synthseg_pc_vs_jlf.sh     # when SSP_GT_DIR / SSP_IMG_DIR set

4. Schaefer — executed¶

Annots bundled under resources/schaefer2018/…. FS wrapper propagates SUBJECTS_DIR.

Wrote lh/rh.schaefer.annot on:

standalone FS2.6 EG subjects
work/eg_gpu_core_lesion/sub-EG

export SUBJECTS_DIR=…/subjects   # must contain fsaverage + sid
python -m dlsurfer run --profile atlas-schaefer --t1 /dev/null --sd "$SUBJECTS_DIR" --sid sub-EG --execute

5. BIDS App¶

Derivatives + Boutiques + CI fixture — see bids_app.md.

6. Metrics vs legacy SLURM¶

python scripts/compare_metrics_slurm.py \
  --metrics work/eg_gpu_core_lesion/sub-EG/scripts/dlsurfer_metrics.tsv \
  --jobid 191960 --out work/eg_gpu_core_lesion/metrics_vs_slurm.json