nv-generate-mr-brain

Used for generating synthetic brain MRI volumes with NV-Generate-CTMR rflow-mr-brain. Not for production training data.

Purpose

Used for generating synthetic brain MRI volumes with NV-Generate-CTMR rflow-mr-brain. Not for production training data.
Use the wrapper exactly as documented; do not replace the upstream entrypoint with a handwritten implementation.
Do not write custom inference code for normal runs. The wrapper owns config staging, output paths, and validation.
Manifest I/O: inputs are model_config_override; outputs are synthetic_mr_brain_volumes and result_json.

Instructions

Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
Run scripts/run_mr_brain.py through the documented command below; keep outputs under a caller-provided run directory.
If a host agent exposes run_script, use run_script("scripts/run_mr_brain.py", args=[...]); otherwise run the Bash/Python command shown below.
Emit a single bash code block, and keep the python -m pip install -r "$NV_GENERATE_ROOT/requirements.txt" step in that same command — the runtime may be a fresh environment without nibabel/MONAI, so dropping the install fails with ModuleNotFoundError.
Do not add rm, mkdir, or any cleanup of --output-dir; the wrapper creates it. Use a fresh --output-dir instead of deleting one.
Check the emitted JSON and paired verifier guidance before treating the run as evidence.

Available Scripts

Script	Purpose	Arguments
`scripts/run_mr_brain.py`	Primary entrypoint declared by skill_manifest.yaml.	`MODEL_CONFIG.json --output-dir OUT_DIR --modality mri_t1 [--random-seed N] [--yes]`

Prerequisites

Runtime requirements: GPU/CUDA when declared by the manifest; Python packages listed in runtime.side_effects.pip_packages.
Side effects: writes generated outputs under the caller's --output-dir, may cache model assets under ~/.cache/huggingface/, and may contact https://huggingface.co or https://github.com during setup.
Run commands from the repository root unless an existing section below says otherwise.

Limitations

This is a thin wrapper. Inference, sampling, and decoding are delegated entirely to NVIDIA-Medtech/NV-Generate-CTMR's scripts.diff_model_infer. Do not modify code under $NV_GENERATE_ROOT or the repo-local fallback at .workbench_data/upstreams/NV-Generate-CTMR.
rflow-mr-brain generates image-only synthetic brain MRI volumes. It does not emit paired segmentation masks.
Output volumes are synthetic. They are not safe as training data for production medtech models without independent quality review.
Not for clinical deployment, clinical interpretation, autonomous diagnosis, regulatory submission.

Troubleshooting

Error	Cause	Fix
Missing dependency or import error	Runtime package drift from `skill_manifest.yaml`.	Install the packages declared in the manifest or use the documented setup command.
Empty or schema-invalid output	Wrong input path, unsupported modality, or upstream failure.	Re-run with a known fixture and inspect the wrapper JSON plus stderr.
Validation gate failure	Output violated a declared engineering invariant.	Keep the failed evidence pack and use the gate message to repair inputs or wrapper code.

Wraps the upstream NVIDIA-Medtech/NV-Generate-CTMR MR brain image-only generation workflow. The wrapper does not reimplement diffusion sampling or autoencoder decoding. It stages config overrides, runs the documented python -m scripts.diff_model_infer command for rflow-mr-brain, then summarizes the generated NIfTI volume.

Exact Runnable Surface

For user run commands, use this repo-root wrapper path exactly:

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 skills/nv-generate-mr-brain/scripts/run_mr_brain.py PATH_TO_MR_BRAIN_CONFIG.json --output-dir OUT_DIR --modality mri_t1 --random-seed 1234

Do not invent generate.sh, infer.py, Medical AI Skills run, or python -m nv_generate_mr_brain commands. PATH_TO_MR_BRAIN_CONFIG.json must be the user's supplied request path.

Preconditions

If NV_GENERATE_ROOT already names a local checkout, the wrapper uses it and records its current commit in the result. Otherwise, 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
pip install -r "$NV_GENERATE_ROOT/requirements.txt"

Download the MR-brain weights:

cd "$NV_GENERATE_ROOT"
python -m scripts.download_model_data --version rflow-mr-brain --root_dir ./ --model_only

Runtime needs an NVIDIA GPU with at least 16 GB VRAM. There is no CPU fallback in the upstream path.

The wrapper also searches .workbench_data/upstreams/NV-Generate-CTMR if NV_GENERATE_ROOT is unset or does not have the required upstream layout.

For agent-generated user run commands, use the command in Usage. Do not prepend clone or model-download setup steps when the repo-local upstream cache already exists. In a fresh Python environment, still include pip install -r "$NV_GENERATE_ROOT/requirements.txt" before the wrapper unless the active environment has already proven those imports are available; cached weights do not imply cached Python packages. If setup requires cd "$NV_GENERATE_ROOT", return to the Medical AI Skills repo before invoking skills/nv-generate-mr-brain/scripts/run_mr_brain.py.

Usage

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 skills/nv-generate-mr-brain/scripts/run_mr_brain.py \
  PATH_TO_MR_BRAIN_CONFIG.json \
  --output-dir runs/nv_generate_mr_brain_demo \
  --modality mri_t1 \
  --random-seed 1234

Replace PATH_TO_MR_BRAIN_CONFIG.json with the user's actual request/config path. Do not copy the fixture path from this document unless the user explicitly asked to run that fixture. If the user says "the request is at runs/.../default_mri_t1.json", that exact path is the first positional argument to scripts/run_mr_brain.py.

Supported MR-brain modality names are mri, mri_t1, mri_t2, mri_flair, mri_swi, mri_t1_skull_stripped, mri_t2_skull_stripped, mri_flair_skull_stripped, and mri_swi_skull_stripped. These map to the upstream configs/modality_mapping.json IDs documented in the README. For FOV and setup details, see references/fov-and-downloads.md.

The fixture argument is a small JSON override for configs/config_maisi_diff_model_rflow-mr-brain.json. Pass default to use the upstream defaults plus the CLI modality and random seed. Common override keys are dim, spacing, num_inference_steps, cfg_guidance_scale, and modality.

Each run records the staged config, model inventory, upstream command, output geometry, spacing, affine, intensity range, and non-constant / finite-data checks. Output volumes are synthetic and are not safe as production training data without independent review.

Not for clinical interpretation, production deployment, autonomous diagnosis, or regulatory submission.

nv-generate-mr-brain