FAQ¶
Is DLSurfer a FreeSurfer replacement?¶
No. It orchestrates FastSurfer / FreeSurfer (and related DL tools) and writes a standard SUBJECTS_DIR.
Why not wire VINN myself?¶
You lose the SUBJECTS_DIR contract, module glue, and HPC seg/surf split. See engine policy.
doctor says READY but login has no GPU¶
Expected. Run VINN/LIT on a GPU allocation; login-node nvidia-smi MISS is fine.
TopoFit fails with CUDA / slow_conv3d¶
FS 7.4.1 SIF torch may not run conv3d on newer GPUs. Use --device cpu for TopoFit.
TopoFit: norm.mgz is not a file¶
surfa rejects symlinks. Hardlink/copy orig_nu.mgz → norm.mgz, or pass a real volume. Prefer --seg_only --tal_reg so talairach.lta exists.
FastSurfer: unrecognized --batch_size¶
Use FastSurfer’s --batch (DLSurfer --batch-size maps correctly in current planner).
Execute blocked by gates¶
dlsurfer gates — use --allow-experimental only for lab overrides, or wait until status is passed.