Latent Space Is Not Flat: Rethinking Latent Structure for 3D Medical Image Synthesis

Latent generative models make 3D medical image synthesis computationally practical by generating in a compressed space. However, we show that the common flat Euclidean assumption induced by ℓ2 objectives is imprecise: latent-space geometry is so strongly anisotropic that equal-magnitude errors can produce drastically different decoded distortions. We further find that this anisotropy has a clear feature: sensitive variation concentrates in a low-rank subspace. The dominant low-rank components capture the overall structure, encoding long-range, spatially coordinated variation while remaining resistant to local noise. Its orthogonal residual, in contrast, mainly captures local and image-specific variation. Motivated by this asymmetry, we introduce Latent Structure Flow (LSF). At each block, LSF decomposes the latent state into structure and residual, models structural changes with global context, and predicts residual variation locally while preserving a direct path for the input structure. LSF changes only the generator, leaving the frozen codec and pointwise training objective unchanged. Across cross-modality synthesis and tumor inpainting tasks, LSF outperforms all compared baselines on both global and tumor-specific metrics, demonstrating the benefit of explicitly modeling latent-space structure for 3D medical image synthesis.