dicom_series_to_volume

Purpose

• Used for converting one CT DICOM series folder to a HU NIfTI volume with affine evidence. Not for multi-frame DICOM or clinical use.
• Use the wrapper exactly as documented; do not replace the upstream entrypoint with a handwritten implementation.
• Manifest I/O: inputs are dicom_dir; outputs are nifti_volume and result_json.

Instructions

• Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
• Run scripts/series_to_volume.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/series_to_volume.py", args=[...]); otherwise run the Bash/Python command shown below.
• Check the emitted JSON and the paired dicom_volume_quality_v1 verifier before treating the run as evidence.

Available Scripts

Script	Purpose	Arguments
scripts/series_to_volume.py	Primary entrypoint declared by skill_manifest.yaml.	PATH_TO_DICOM_DIR [--output OUT.nii.gz]

Prerequisites

• Runtime requirements: Python packages listed in runtime.side_effects.pip_packages.
• NiBabel 5.4 or newer is required so extreme-oblique axes remain labeled consistently across reorientation.
• Run commands from the repository root unless an existing section below says otherwise.

Limitations

• Single-series only; multi-series input is rejected at preflight.
• Multi-frame DICOM (NumberOfFrames > 1 per file) not supported.
• Compressed transfer syntaxes (JPEG / JPEG2000 / RLE) not supported.
• No voxel reorientation. The affine is derived from DICOM headers and represented in NIfTI/RAS coordinates; a downstream gate (e.g. expected_axcodes) is expected to assert orientation before this volume is fed to a segmentation model.
• Not for clinical deployment, autonomous diagnosis, regulatory submission, production inference (use a vetted converter such as dcm2niix for that).

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.

Reads one DICOM series, sorts slices by ImagePositionPatient, applies RescaleSlope and RescaleIntercept, builds an affine from orientation and spacing tags, and writes a .nii.gz plus JSON summary.

python scripts/series_to_volume.py PATH_TO_DICOM_DIR --output PATH_TO_OUT.nii.gz

For a trusted run with the paired verifier:

python -m eval_engine.run_trusted skills/dicom-series-to-volume \
  --fixture PATH_TO_DICOM_DIR \
  --out runs/dicom_series_to_volume_trusted

Key output fields: n_slices, series_instance_uid, output.path, output.shape, output.spacing, output.axcodes, output.affine, hu_range, and runtime.conversion_seconds.

Scope limits: single-series CT only; no multi-frame DICOM, compressed transfer syntax handling, RT structure sets, auto-reorientation, or clinical use.