NV-Generate-VAE-Finetune

Purpose

• Used for finetuning the NV-Generate-CTMR MAISI VAE/autoencoder from user-supplied CT or MRI NIfTI training volumes.
• Not for clinical interpretation, regulatory use, or approving synthetic data for production training.
• Upstream currently documents VAE training in train_vae_tutorial.ipynb and provides configs/helpers, but not a scripts.train_vae CLI. This skill does not execute the notebook; it stages the required config/datalist glue locally and uses upstream helper APIs.
• Manifest I/O: inputs are datalist and data_base_dir; outputs are autoencoder_checkpoint, discriminator_checkpoint, and result_json.
• The underlying training contract is the upstream config/env JSON (config_maisi_vae_train.json + environment_maisi_vae_train.json, as used in train_vae_tutorial.ipynb). The wrapper stages those JSON files for you and exposes the most-tuned fields as CLI flags; the sections below document the fields, their defaults, and how to monitor/tune a run.

Instructions

• Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
• Run scripts/run_vae_finetune.py from the Medical AI Skills repo root.
• If a host agent exposes run_script, use run_script("scripts/run_vae_finetune.py", args=[...]); otherwise run the Bash/Python command below.
• Use --preflight first when checking a new datalist; remove --preflight only when the user explicitly wants to launch GPU finetuning.
• For a staged preflight input bundle directory, use BUNDLE/preflight_datalist.json as the datalist and BUNDLE/preflight_dataset as --data-base-dir when those files are present.

Examples

Validate and stage a preflight finetune check from an input bundle (the recommended first step — no GPU, no training). This is the single canonical command; replace INPUT_BUNDLE and OUT_DIR with your paths: