NV-Segment-CT Finetune

Purpose

Used for smoke or dataset finetuning of NV-Segment-CT VISTA3D on CT NIfTI labels. Not for clinical validation.
Wraps the upstream MONAI bundle entrypoint; do not replace it with handwritten training or inference code.
Manifest inputs are dataset_dir, datalist, target_anatomy, label_mapping, smoke, sanity, auto_seg, and skip_formal_eval.
Manifest outputs are finetuned_ckpt and schema-checked result_json.

Run scripts/run_finetune.py; do not patch files under bundle/ or upstream checkouts during normal skill use.
For standalone Bash, include the fresh-environment setup line before the wrapper; benchmark venvs start empty.
Run the committed script in place from the repo root. Do not copy this skill to a runtime directory, and do not use rm or cleanup commands in generated invocations.
If a host exposes run_script, use run_script("scripts/run_finetune.py", args=[...]); otherwise run from the repo root.
For the shortest workflow check, use --smoke; for MSD Task06 Lung Tumor reproduction, use --sanity.
Read references/task06-and-results.md only when you need Task06 reference details, output-field definitions, or manual bundle setup notes.