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nv-segment-ct

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Updated 10-16 04:34

About this skill

NV-Segment-CT

Purpose

  • Used for running NV-Segment-CT VISTA3D on CT 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_volume; outputs are label_map and result_json.

Instructions

  • Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
  • Run scripts/run_vista3d.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_vista3d.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

Script Purpose Arguments
scripts/run_vista3d.py Primary entrypoint declared by skill_manifest.yaml. PATH_TO_CT.nii.gz [--output-dir OUT_DIR] [--label-prompts IDS]

Prerequisites

  • Runtime requirements: GPU/CUDA when declared by the manifest; Python packages listed in runtime.side_effects.pip_packages.
  • Side effects: writes the downloaded bundle under skills/nv-segment-ct/bundle/, may cache model assets under ~/.cache/huggingface/, and may contact https://huggingface.co during first setup; the optional spleen fixture fetcher downloads MSD09 from https://msd-for-monai.s3-us-west-2.amazonaws.com.
  • 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 official hugging_face_pipeline.HuggingFacePipelineHelper in bundle/. Do not modify code under bundle/.
  • transformers must be a 4.x release; the HF model code uses pre-5.x idioms (e.g. _tied_weights_keys).
  • Device auto-detected (cuda if available, else cpu); --device flag overrides.
  • Output may be schema-valid but semantically empty (e.g. label prompts that do not match the input anatomy). Sanity gates assert at least one foreground voxel per requested anatomy.
  • 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/NV-Segment-CT helper. The wrapper does not reimplement VISTA3D inference.

Exact Runnable Surface

For CT segmentation user runs, use this repo-root wrapper path exactly:

python skills/nv-segment-ct/scripts/run_vista3d.py PATH_TO_CT.nii.gz --label-prompts "1,3,5,14" --output-dir OUT_DIR

Do not invent infer.py, Medical AI Skills run, python -m nv_segment_ct, or anatomy-name-only flags. For spleen, liver, right kidney, and left kidney, the required VISTA3D label IDs are exactly 1,3,5,14.

Preconditions

The skill assumes a Python 3.12 environment with no pre-installed runtime deps — its documented command installs everything it needs. Pinned dep list is at requirements.txt.

Two one-time downloads (the documented command does the first one; the fixture fetch is a separate step you run when bootstrapping):

# Spleen example fixture from Decathlon MSD09 (~1.5 GB tar, ~11 MB
# fixture extracted into skills/nv-segment-ct/fixtures/spleen_03.nii.gz):
python skills/nv-segment-ct/fixtures/fetch_spleen_fixture.py

Both downloads (the bundle below, and the fixture) are gitignored (Medical AI Skills policy: no medical data or model weights in git). The fetch script is idempotent and caches the tar under .workbench_data/datasets/ so re-runs are no-ops.

Runtime needs an NVIDIA GPU with CUDA. CPU fallback is supported but slow.

Usage

From Medical AI Skills repo root, run all steps in a single command so the skill is self-bootstrapping against a fresh Python 3.12 venv:

pip install -r skills/nv-segment-ct/requirements.txt && \
huggingface-cli download nvidia/NV-Segment-CT \
  --local-dir skills/nv-segment-ct/bundle/ && \
python skills/nv-segment-ct/scripts/run_vista3d.py PATH_TO_CT.nii.gz \
  --label-prompts "1,3,5,14" \
  --output-dir vista3d_outputs

When the user names anatomies, translate them to VISTA3D class IDs before running. For the common abdominal CT request:

Anatomy VISTA3D class ID
liver 1
spleen 3
right kidney 5
left kidney 14

For "segment the spleen, liver, right kidney, and left kidney", the correct --label-prompts value is exactly "1,3,5,14". Do not substitute kidney IDs from another label dictionary; the wrapper validates the requested label set and will mark the run invalid if the emitted mask contains labels outside the requested set.

The pip install step is load-bearing: do not assume monai/torch/etc. are already in the active environment. The huggingface-cli download step is also part of the contract — it pulls the ~832 MB model bundle into skills/nv-segment-ct/bundle/ (cached after first run; subsequent calls are no-ops).

label-prompts are VISTA3D class IDs. The evidence output records input geometry, output mask path, observed label IDs, unexpected labels, per-class voxel counts, per-class physical volumes computed from the output mask header spacing, runtime, model identity, and fixed code-derived artifact checks such as mask shape, affine match, label set, foreground count, and class-volume bounds.

Pass --ground-truth PATH to record a reference label-map path under input.ground_truth_path. The skill does not compute Dice; that is the paired verifier's job.

Anatomy plausibility (per-class volume bounds, fragmentation, bilateral symmetry, liver larger than spleen) and optional per-class Dice/IoU against the recorded ground truth are checked by verifiers/ct_segmentation_quality_v1.

Not for clinical interpretation, production deployment, or non-CT modalities.