Exploiting Completeness Perception with Diffusion Transformer for Unified 3D MRI Synthesis

Missing data problems, such as missing modalities in multi-modal brain MRI and missing slices in cardiac MRI, pose significant challenges in clinical practice. Existing methods rely on external guidance to supply detailed missing-state information for instructing generative models to synthesize missing MRIs. However, manual indicators are not always available or reliable in real-world scenarios due to the unpredictable nature of clinical environments. Moreover, these explicit masks are not informative enough to provide guidance for improving semantic consistency. In this work, we argue that generative models should infer and recognize missing states in a self-perceptive manner, enabling them to better capture subtle anatomical and pathological variations. Towards this goal, we propose CoPeDiT, a shared completeness-perception framework for 3D MRI synthesis, following a common conditioning strategy with task-specific instantiations for different missing-data scenarios. Specifically, we incorporate dedicated pretext tasks into our tokenizer, CoPeVAE, empowering it to learn completeness-aware discriminative prompt tokens, and design MDiT3D, a specialized diffusion transformer architecture for 3D MRI synthesis that effectively uses the completeness-aware prompt tokens as guidance to enhance semantic consistency in 3D space. Comprehensive evaluations on three large-scale MRI datasets demonstrate that CoPeDiT consistently improves upon state-of-the-art methods across diverse missing patterns, yielding high-fidelity and structurally consistent MRI synthesis. Our code is available at https://github.com/JK-Liu7/CoPeDiT.