dicom-series-to-volume

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Translated

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Used for converting one CT DICOM series folder to a HU NIfTI volume with affine evidence. Not for multi-frame DICOM or clinical use.

3installs

Sourcenvidia/skills

Added on2026-06-01

NPX Install

npx skill4agent add nvidia/skills dicom-series-to-volume

SKILL.md Content

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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
```
.
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.

bash

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

For a trusted run with the paired verifier: