seg2med: a bridge from artificial anatomy to multimodal medical images

Abstract

We present seg2med, a modular framework for anatomy-driven multimodal medical image synthesis. The system integrates three components to enable high-fidelity, cross-modality generation of CT and MR images based on structured anatomical priors. First, anatomical maps are independently derived from three sources: real patient data, XCAT digital phantoms, and synthetic anatomies created by combining organs from multiple patients. Second, we introduce PhysioSynth, a modality-specific simulator that converts anatomical masks into prior volumes using tissue-dependent parameters (e.g., HU, T1, T2, proton density) and modality-specific signal models. It supports simulation of CT and multiple MR sequences including GRE, SPACE, and VIBE. Third, the synthesized anatomical priors are used to train 2-channel conditional denoising diffusion models, which take the anatomical prior as structural condition alongside the noisy image, enabling generation of high-quality, structurally aligned images. The framework achieves SSIM of 0.94 for CT and 0.89 for MR compared to real data, and FSIM of 0.78 for simulated CT. The generative quality is further supported by a Frechet Inception Distance (FID) of 3.62 for CT synthesis. In modality conversion, seg2med achieves SSIM of 0.91 for MR to CT and 0.77 for CT to MR. Anatomical fidelity evaluation shows synthetic CT achieves mean Dice scores above 0.90 for 11 key abdominal organs, and above 0.80 for 34 of 59 total organs. These results underscore seg2med's utility in cross-modality synthesis, data augmentation, and anatomy-aware medical AI.