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dce2bids Integration

dce2bids is the petmri group's DICOM-to-BIDS conversion tool for DCE-MRI studies. It is the recommended way to convert raw DICOM data into the BIDS layout DCEPrep expects. It is more automated, but has less control than the bundled sort_dicom.py script for new studies.

Why dce2bids

Every scanner and protocol labels its series and parameters a little differently. Instead of maintaining a hand-edited series-matching config per site (as sort_dicom.py requires), dce2bids uses a coding agent (Claude Code, Codex, VS Code with Copilot, or Cursor) to work out the correct settings once per scanner/protocol, following the rules and validation steps defined in the tool's SKILL.md. After that one-time, AI-assisted setup, converting each new participant on that scanner/protocol is a single command — no AI needed.

Only the series DCEPrep needs are converted: the dynamic DCE series, the VFA flip-angle scans, and one structural scan (usually a T1 MPRAGE). Everything else in the session is left out.

Integration with DCEPrep

dce2bids is a standalone tool that produces a BIDS dataset. DCEPrep itself only consumes BIDS-organized data — it does not call dce2bids directly, so any BIDS dataset produced by dce2bids that matches the required file patterns will work.

How-To