Gaps remaining without a credible alternative¶

These COMPARE gaps have no best alternative implemented (and often none that belong in DLSurfer).
Everything else from COMPARE_FS_FASTSURFER.md now has a wired best alternative (profile, flag, or engine).

Run: dlsurfer gaps-remaining

Gap	Why no alternative in DLSurfer	What to do instead
Dedicated DLSurfer meta-container (SIF/Docker)	Packaging/ops only — not a morphometry method. No separate science tool substitutes for “our” image.	Use pinned FastSurfer image + host FS; scaffold `containers/dlsurfer.def`
*Manual edit loops (`-autorecon2-`)**	Interactive QC by design; automation would fight FreeSurfer’s edit model	FreeView + targeted `recon-all -autorecon2-*` outside DLSurfer
Full QC GUI (FreeView workflows)	GUI is FreeSurfer’s product; DLSurfer is CLI orchestration	Open SUBJECTS_DIR in FreeView
TRACULA / PET / fMRI helper streams	Explicitly out of scope (diffusion/PET/fMRI ≠ T1 morphometry orchestrator)	Use FreeSurfer / modality-specific pipelines
Bit-identical `recon-all` reproducibility claim	Non-claim: FastSurfer/DLSurfer do not promise bit-identity with classical recon-all	Prefer FS8 profile if you need classical FS tree semantics
True Infant FreeSurfer neonate stream	Only partially covered: `fs-clinical` = clinical/odd-contrast, not Infant FS	Install Infant FreeSurfer separately (documented runner-up under `recon_all_clinical`)
Native LIT + optimal GPU/CPU seg↔surf split	Upstream FastSurfer constraint (`--lesion_mask` blocks `--seg_only`/`--surf_only`) — not solvable by another engine	Prefer profile `core-lesion` (standalone neuroLIT)

Explicitly not “missing alternatives”¶

These looked like gaps but now have a chosen best alternative wired:

Former gap	Best alternative	How
DK / `--fsaparc`	FastSurfer `--fsaparc`	`--atlas dk` or profile `core-dk`
Destrieux	FS `-a2009s`	profile `atlas-destrieux`
Schaefer / MMP-style	`mri_surf2surf` annot project	profile `atlas-schaefer` (MMP same pattern)
Longitudinal	FS `-base` / `-long`	profile `fs-long`
HA subfields	`segmentHA_T1.sh`	profile `subfields-ha` (+ HippUnfold/Hippodeep as runners-up)
Brainstem / thalamic	`segmentBS` + `segmentThalamicNuclei`	profile `nuclei-bs-thal`
Clinical / odd contrast	`recon-all-clinical`	profile `fs-clinical`
Module toggles	FastSurfer `--no_*`	`--no-cc` / `--no-cereb` / `--no-hypothal`
HPC `srun` / `brun`	Upstream wrappers	`--hpc srun\\|brun`
High-res VINN	FastSurfer `--vox_size`	`--vox-size <mm>`
DL surfaces / fast thickness	TopoFit / V2C-Flow / SUGAR / DL-CTE	existing Phase 3 experimental profiles