---name: nv-generate-vae-finetunedescription: Used for finetuning the NV-Generate-CTMR MAISI VAE from CT/MRI NIfTI datalists. Not for clinical or production data approval.license: Apache-2.0allowed-tools: Bashmetadata: author: NVIDIA MedTech Teamtags: ---

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:

export NV_GENERATE_ROOT="${NV_GENERATE_ROOT:-$HOME/.cache/nvidia-skills/upstreams/NV-Generate-CTMR-61c4ec7}" && \
python skills/nv-generate-vae-finetune/scripts/run_vae_finetune.py \
  INPUT_BUNDLE/preflight_datalist.json \
  --data-base-dir INPUT_BUNDLE/preflight_dataset \
  --output-dir OUT_DIR \
  --modality mri \
  --preflight

For real GPU finetuning and other variations, see Usage below.

Available Scripts

Script	Purpose	Arguments
scripts/run_vae_finetune.py	Primary entrypoint declared by skill_manifest.yaml.	DATALIST.json --data-base-dir DATA_DIR --output-dir OUT_DIR [--epochs N] [--modality mri] [--patch-size 64,64,64] [--preflight]

Prerequisites

• An explicit NV_GENERATE_ROOT may point to the caller's local checkout and must contain configs/config_maisi_vae_train.json, scripts/transforms.py, and scripts/utils.py. The result records its current commit.
• If NV_GENERATE_ROOT is unset, the wrapper searches .workbench_data/upstreams/NV-Generate-CTMR.
• CUDA_VISIBLE_DEVICES is optional and can be used to select the GPU for real training.
• Runtime requirements: NVIDIA CUDA GPU for real training, Python packages from the upstream requirements.txt, lpips, and downloaded VAE weights unless using --train-from-scratch.
• Side effects: writes staged configs, checkpoints, TensorBoard logs, and run summaries under the caller-provided --output-dir; may write model caches under the upstream checkout, ~/.cache/huggingface/, and ~/.cache/torch/; may contact https://huggingface.co, https://github.com, and https://download.pytorch.org.
• The datalist is a MONAI-style JSON object with non-empty training[] and validation[] or testing[]. Each entry has an image path relative to --data-base-dir and optional class or modality of ct or mri.

When no local checkout is supplied, create the recommended pinned default checkout once:

if [ -z "${NV_GENERATE_ROOT:-}" ]; then
  export NV_GENERATE_COMMIT=61c4ec709b84cad468852243c48e250bec732074
  export NV_GENERATE_ROOT="$HOME/.cache/nvidia-skills/upstreams/NV-Generate-CTMR-61c4ec7"
  if [ ! -d "$NV_GENERATE_ROOT/.git" ]; then
    git clone https://github.com/NVIDIA-Medtech/NV-Generate-CTMR.git "$NV_GENERATE_ROOT"
    git -C "$NV_GENERATE_ROOT" checkout --detach "$NV_GENERATE_COMMIT"
  fi
fi

1. Config and environment JSON (adapt to your data)

The wrapper copies the upstream VAE config/env JSON from $NV_GENERATE_ROOT/configs, rewrites the fields below, and writes the staged copies under OUT_DIR/workflow/configs/. You normally only set your datalist and data root; the listed CLI flags override individual fields when you need to.

Environment JSON (environment_maisi_vae_train.json):

Field	Set from	Notes
model_dir	--output-dir	Where autoencoder.pt/discriminator.pt and best checkpoints are saved.
tfevent_path	--output-dir	TensorBoard event directory.
finetune	--train-from-scratch	true (default) loads trained_autoencoder_path; the flag sets it false.
trained_autoencoder_path	upstream weights / --trained-autoencoder-path	Starting VAE checkpoint when finetuning.

Training fields (config_maisi_vae_train.json):

Field	Flag	Type	Default	Notes
autoencoder_train.n_epochs	--epochs	int	1
autoencoder_train.batch_size	--batch-size	int	1	Per-GPU (single-GPU runner).
autoencoder_train.patch_size	--patch-size	int,int,int	64,64,64	Training crop.
autoencoder_train.val_batch_size	--val-batch-size	int	1
autoencoder_train.val_sliding_window_patch_size	--val-sliding-window-patch-size	int,int,int	96,96,64	Sliding-window validation ROI.
autoencoder_train.lr	--lr	float	1e-4
autoencoder_train.perceptual_weight	--perceptual-weight	float	0.3	LPIPS term.
autoencoder_train.kl_weight	--kl-weight	float	1e-7	KL term.
autoencoder_train.adv_weight	--adv-weight	float	0.1	Adversarial term.
autoencoder_train.recon_loss	--recon-loss	l1|l2	l1
autoencoder_train.val_interval	--val-interval	int	1	Epochs between validation passes.
autoencoder_train.cache	--cache-rate	float	0.0	MONAI CacheDataset fraction.
autoencoder_train.amp	--no-amp	flag	on	Mixed precision; flag disables it.
data_option.random_aug	--no-random-aug	flag	on	Random augmentation; flag disables it.
data_option.spacing_type	--spacing-type	original|fixed|rand_zoom	original
data_option.spacing	--spacing	float,float,float	unset	Required when spacing_type is fixed/rand_zoom.
data_option.select_channel	--select-channel	int	0	Channel for multi-channel inputs.

--modality (ct or mri, default mri) fills the per-entry class for datalist items missing one. Validation/testing entries are required because the training loop runs a validation pass.

For an end-to-end reference including example data download, see the upstream tutorial train_vae_tutorial.ipynb.

2. Usage (one-line training)

Preflight only:

export NV_GENERATE_ROOT="${NV_GENERATE_ROOT:-$HOME/.cache/nvidia-skills/upstreams/NV-Generate-CTMR-61c4ec7}" && \
python skills/nv-generate-vae-finetune/scripts/run_vae_finetune.py \
  PATH_TO_DATALIST.json \
  --data-base-dir PATH_TO_DATA_ROOT \
  --output-dir runs/nv_generate_vae_finetune_preflight \
  --preflight

Preflight bundle input:

export NV_GENERATE_ROOT="${NV_GENERATE_ROOT:-$HOME/.cache/nvidia-skills/upstreams/NV-Generate-CTMR-61c4ec7}" && \
python skills/nv-generate-vae-finetune/scripts/run_vae_finetune.py \
  PATH_TO_INPUT_BUNDLE/preflight_datalist.json \
  --data-base-dir PATH_TO_INPUT_BUNDLE/preflight_dataset \
  --output-dir runs/nv_generate_vae_finetune_preflight \
  --preflight

GPU finetuning:

export NV_GENERATE_ROOT="${NV_GENERATE_ROOT:-$HOME/.cache/nvidia-skills/upstreams/NV-Generate-CTMR-61c4ec7}" && \
python -m pip install -r "$NV_GENERATE_ROOT/requirements.txt" && \
python -m pip install lpips tensorboard && \
python skills/nv-generate-vae-finetune/scripts/run_vae_finetune.py \
  PATH_TO_DATALIST.json \
  --data-base-dir PATH_TO_DATA_ROOT \
  --output-dir runs/nv_generate_vae_finetune \
  --epochs 1 \
  --modality mri \
  --patch-size 64,64,64 \
  --download-model-data

Replace PATH_TO_DATALIST.json and PATH_TO_DATA_ROOT with the user's actual paths. Do not use the fixture datalist for real training; it is a preflight-only placeholder.

3. Monitor training (TensorBoard)

The runner writes TensorBoard scalars (per-iteration and per-epoch recons_loss, kl_loss, p_loss, adversarial/real/fake losses, and a validation scale_factor) under OUT_DIR/artifacts/tfevent/autoencoder. Launch TensorBoard against the output directory:

python -m pip install tensorboard && \
tensorboard --logdir runs/nv_generate_vae_finetune/artifacts/tfevent

The same per-epoch loss history is also captured in OUT_DIR/artifacts/workflow_summary.json and echoed in the JSON the wrapper prints to stdout (loss_history, best-checkpoint paths, exit_code, stderr_tail).

4. Hyperparameter tuning and common pitfalls

• Reconstructions blurry — raise --perceptual-weight (default 0.3); try --recon-loss l2 if edges look washed out.
• Posterior collapse / over-regularized latents — --kl-weight is intentionally tiny (1e-7); increasing it too much degrades reconstruction.
• Adversarial training unstable — lower --adv-weight (default 0.1) or --lr; a warmup schedule already ramps the LR over the first 20 epochs.
• Out-of-memory — reduce --patch-size (e.g. 48,48,48) and --val-sliding-window-patch-size, keep --batch-size 1, and lower --cache-rate.
• datalist must include non-empty validation[] or testing[] — the validation loop is mandatory; add validation[] (or testing[]) entries.
• Single-GPU only — the runner asserts exactly one CUDA GPU; set CUDA_VISIBLE_DEVICES to pick which one.

5. Evaluate the finetuned VAE

Validation reconstruction loss (lowest-val_weighted_loss epoch) is tracked automatically and the best autoencoder is saved as autoencoder_epochN.pt under OUT_DIR/artifacts/models. To evaluate downstream:

• Compare validation recons_loss/p_loss curves across runs in TensorBoard, and
• Plug the finetuned autoencoder into a diffusion finetune/generation run (e.g. nv-generate-mr-brain-finetune via --trained-autoencoder-path) to confirm latents still decode to usable volumes.

This skill gates file accounting and reconstruction bookkeeping only — image quality and downstream utility must be judged by a domain expert.

Limitations

• Requires a current upstream NV-Generate-CTMR checkout with VAE configs and helper APIs. The skill owns the runner glue and does not depend on the notebook.
• Full training can be expensive and is not deterministic across hardware, CUDA, and package versions.
• The wrapper gates file accounting and command provenance, not anatomical realism, reconstruction quality, or downstream model utility.
• Not for clinical deployment, clinical interpretation, autonomous diagnosis, regulatory submission, or production training-data approval.

Troubleshooting

Error	Cause	Fix
VAE configs/helpers were not found	NV_GENERATE_ROOT does not point at a current NV-Generate-CTMR checkout.	Clone or update https://github.com/NVIDIA-Medtech/NV-Generate-CTMR and set NV_GENERATE_ROOT.
datalist must include non-empty validation[] or testing[]	VAE training requires validation data for the configured validation loop.	Add validation[] or testing[] entries with relative image paths.
CUDA, MONAI, or LPIPS import failure	Runtime environment lacks upstream dependencies.	Install "$NV_GENERATE_ROOT/requirements.txt" plus lpips tensorboard in the selected environment.