NV-Generate-MR-Brain

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.