Specialty structure + Synth* preprocess modules

Optional engines that fill anatomy not in default FastSurferVINN / DKT.
Orchestrator-only — code stays in this folder; weights/tools live under lab Documents/.

Profile	Engine	Lab path	Status
preprocess-synthsr	synthsr (mri_synthsr)	FS / piriform/synthseg_pc/maybe_synthsr.sh	P preprocess only
structure-claustrum	mauri_claustrum	Documents/clau_seg	P
structure-piriform-synthseg	synthseg_pc	Documents/piriform/synthseg_pc	E until JLF gate
structure-hippunfold	hippunfold	Documents/HippUnfold	R (HA alt)
clinical-claustrum	SynthSR → Mauri	both	P chain

Hard rules

1. Mauri claustrum ≠ piriform. Never run claustrum weights as Steinbart 125/126.
2. SynthSeg-PC ≠ mri_synthseg. Stock FreeSurfer SynthSeg has no PC class.
3. SynthSR does not segment PC or claustrum — T1 salvage only.
4. IDEAS production PC stays JLF until SynthSeg-PC / nnU-Net clears the documented eval bar (piriform claims).
5. Isolation: no DKT connectome imports; write under DLSurfer --sd/--sid.

Env for SynthSeg-PC dry-run → execute

export SYNTHSEG_PC_ROOT=/path/to/Documents/piriform/synthseg_pc
export SYNTHSEG_PC_MODEL=/path/to/weights.h5
export SYNTHSEG_PC_LABELS=/path/to/segmentation_labels.npy
export SYNTHSEG_ROOT=/path/to/Documents/clau_seg/tools/SynthSeg   # or CLAU_SEG_ROOT

Alternatives (PC)

Chosen experimental: SynthSeg-PC. Documented runners-up: JLF (production), MAPER (Steinbart paper), nnU-Net PC (research scaffold).

dlsurfer engines --id synthseg_pc
dlsurfer engines --id mauri_claustrum
dlsurfer cite --profile structure-claustrum