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How to review PET/CT fusion and align it manually with Voxenra

Fuse PET and CT in slices and 3D, adjust the blend, and register the two volumes by hand.

Who it is forA nuclear medicine or imaging researcher who needs to check where PET activity sits on the CT anatomy.

The problemPET and CT are acquired separately, so the two datasets can be misaligned and need a fusion view with manual correction.

The outcomeA fused view of CT, PET and MIP with a rigidly registered PET volume, adjustable colour table and blend ratio, and a 3D fusion view.

What you need first

  • Python with uv installed, so the README command `uv run voxenra` works
  • Local DICOM, NRRD or PACS-accessible CT, MR or PET/CT data you are allowed to use
  • For AI auto-segmentation: a separately installed TotalSegmentator environment and CT fast model, detected under Settings → AI
  • A desktop OS: macOS Apple Silicon or Windows x64 release builds are listed, or a source checkout run with uv

Steps

  1. Clone the repo from https://github.com/l5769389/voxenra and enter the folder.
  2. Run uv run voxenra and import the paired CT and PET series.
  3. Open the PET/CT fusion view and choose the three-plane slice mode.
  4. Adjust the colour table and the fusion ratio, then apply a manual rigid registration until the anatomy lines up.
  5. Switch to the fused 3D view and control the CT and PET display separately.

Prompt for your agent

Work in the repo l5769389/voxenra. Run `uv run voxenra`, import the PET and CT series at <path to PET/CT study>, and open the fusion view. Report whether the PET overlay aligns with CT anatomy at the slice you chose, and state the blend ratio used.

Caveat. The README says PET quantification depends on the image metadata, and dynamic or gated PET is not supported.

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