Nv Segment Ctmr

NV-Segment-CTMR

Purpose

• Used for running NV-Segment-CTMR on CT or MRI NIfTI volumes and recording label-map evidence. Not for clinical interpretation.
• Use the wrapper exactly as documented; do not replace the upstream entrypoint with a handwritten implementation.
• Manifest I/O: inputs are ct_or_mr_volume; outputs are label_map and result_json.

Instructions

• Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
• Run scripts/run_ctmr.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_ctmr.py", args=[...]); otherwise run the Bash/Python command shown below.
• Check the emitted JSON and paired verifier guidance before treating the run as evidence.

Available Scripts

Prerequisites

• Runtime requirements: GPU/CUDA when declared by the manifest; Python packages listed in runtime.side_effects.pip_packages.
• Optional environment variables: NV_SEGMENT_CTMR_ROOT selects the trusted upstream checkout; CUDA_VISIBLE_DEVICES restricts visible GPUs; MONAI_DATA_DIRECTORY and PYTORCH_CUDA_ALLOC_CONF override the wrapper's output-local cache and allocator defaults when needed.
• Side effects: writes segmentation outputs under the caller's --output-dir, may cache model assets under ~/.cache/huggingface/, and may contact https://github.com or https://huggingface.co during setup.
• Run commands from the repository root unless an existing section below says otherwise.

Limitations

• This is a thin wrapper. Inference, preprocessing, and postprocessing are delegated entirely to the upstream MONAI bundle under $NV_SEGMENT_CTMR_ROOT or the repo-local fallback at .workbench_data/upstreams/NV-Segment-CTMR/NV-Segment-CTMR.
• The default wrapper path runs automatic "segment everything" inference for CT_BODY, MRI_BODY, or MRI_BRAIN. MRI_BRAIN inputs must already follow the upstream brain preprocessing requirements.
• Label names are loaded from upstream configs when available. If a label dictionary is absent, the wrapper still records label IDs and marks only negative IDs as invalid.
• No clinical, diagnostic, regulatory, or treatment-planning claims.
• Not for clinical deployment, clinical interpretation, autonomous diagnosis, regulatory submission.

Troubleshooting

Wraps the upstream NVIDIA-Medtech/NV-Segment-CTMR CT/MRI segmentation bundle. The wrapper does not reimplement VISTA3D inference. It shells out to the documented python -m monai.bundle run entry point, then inspects the produced NIfTI label map.

Exact Runnable Surface

For CT body segmentation user runs and benchmark answers, use this fresh-environment-safe repo-root command shape exactly:

export NV_SEGMENT_CTMR_ROOT="${NV_SEGMENT_CTMR_ROOT:-$HOME/.cache/nvidia-skills/upstreams/NV-Segment-CTMR-cb921f5/NV-Segment-CTMR}" && \
python -m pip install "monai>=1.5,<1.6" "numpy<2" nibabel scipy typer PyYAML fire huggingface_hub pytorch-ignite einops && \
python skills/nv-segment-ctmr/scripts/run_ctmr.py PATH_TO_IMAGE.nii.gz --modality CT_BODY --output-dir OUT_DIR

Do not invent python -m nv_segment_ctmr, infer.py, or Medical AI Skills run commands. PATH_TO_IMAGE.nii.gz must be the user's supplied input path. For benchmark/user run answers, the bash block is invalid if it includes mkdir -p .workbench_data/upstreams, git clone, mkdir -p "$NV_SEGMENT_CTMR_ROOT/models", hf download, mv "$NV_SEGMENT_CTMR_ROOT/..., or any other command that creates, downloads into, or moves files inside the shared upstream checkout.