DICOM Processing

Overview

Pipeline skill for converting, reading, and de-identifying medical images in DICOM and NIfTI formats. Encodes deterministic commands and code for:

• DICOM → NIfTI conversion with dcm2niix (including BIDS sidecars)
• Reading DICOM headers and pixel data with pydicom
• PHI removal (de-identification) with pydicom or CTP DicomAnonymizer
• NIfTI inspection with nibabel
• Batch processing grouped by SeriesInstanceUID
• BIDS-compliant directory organization

Use this skill whenever the user works with .dcm, .nii, .nii.gz, DICOM directories, or anonymization workflows.

Usage

1. Convert a DICOM series to NIfTI (dcm2niix)