Diffusion models have become essential for high-fidelity 3D MRI synthesis, yet their deployment remains constrained by substantial GPU resource demands arising from hundreds of U-Net evaluations per sample and a highly heterogeneous kernel behavior. This paper performs a comprehensive performance analysis of the state-of-the-art medical diffusion model, Med-DDPM, across three generations of NVIDIA architectures to study kernel-level runtime breakdowns, instruction-mix characteristics, memory system utilization, warp-level activities, and profiler priority-score estimates. We show that training is overwhelmingly dominated by cuDNN convolution and implicit-GEMM kernels, with inefficiencies arising from memory-access patterns, tensor-layout conversions, and limited Tensor Core utilization. Guided by these insights, we evaluate two architecture-aware optimizations TF32 Tensor Core activation and a 3D channels-last layout and demonstrate that they reduce SM cycles by up to 100x, cut dynamic instructions by 100x, raise Tensor Core utilization from 1.45 to 9.98x, and increase IPC by 7% on A100, all without degrading synthesis quality.
Diffusion models produce high-quality synthetic data but suffer from slow inference. We propose 3D Variable-Step Denoising Diffusion Probabilistic Model (VS-DDPM) a framework engineered to maintain generative quality while accelerating inference by several factors. We tested our approach on four tasks (missing MRI, tumor removal, MRI-to-sCT, and CBCT-to-sCT) within the BraTS2025 and SynthRAD2025 challenges. Designed for high efficiency under hardware and time constrains imposed by both challenges. VS-DDPM achieved state-of-the-art (SOTA) performance in missing MRI synthesis, yielding Dice scores of 0.80, 0.83, and 0.88 for the enhancing tumor, tumor core, and whole tumor regions, respectively, alongside a structural similarity index (SSIM) of 0.95. For MRI tumor removal, the model attained a root mean squared error (RMSE) of 0.053, a peak signal-to-noise ratio (PSNR) of 26.77, and an SSIM of 0.918. While the framework demonstrated competitive performance in MRI-to-sCT and CBCT-to-sCT tasks, it did not reach SOTA benchmarks, potentially due to sensitivities in data pre and post-processing pipelines or specific loss function configurations. These results demonstrate that VS-DDPM provides a robust and tunable solution for high-fidelity 3D medical image synthesis. The code is available in https://github.com/andre-fs-ferreira/SynthRAD_by_Faking_it.
Diffusion models have demonstrated superior fidelity for medical image-to-image translation, but their extension to high-resolution 3D volumes is severely constrained by prohibitive computational cost and GPU memory requirements. Existing memory-efficient strategies often compromise global volumetric consistency or fine anatomical detail. In this work, we propose the Pixel Puzzling Diffusion Model (PPDM), a simple and effective framework for memory- and speed-efficient 3D medical image translation. PPDM introduces a reversible pixel puzzle-unpuzzle operator that trades spatial resolution for channel dimensionality, substantially reducing activation memory while preserving global context. To further improve efficiency and stability, we adopt a direct bridge diffusion formulation that starts from the conditional input rather than pure noise, enabling the model to focus on task-relevant residuals. In addition, a puzzle-gradient loss is incorporated to enforce spatial coherence and suppress grid-like artifacts introduced by spatial rearrangement. We evaluate PPDM on multiple challenging 3D medical image translation tasks, including low-count PET denoising, joint PET denoising and attenuation correction, and cross-modal MRI translation. Across all tasks, PPDM consistently matches or outperforms full 3D diffusion models while reducing training GPU memory usage by up to an order of magnitude and significantly accelerating inference, and it outperforms existing memory-efficient diffusion approaches based on latent compression or frequency decomposition. These results demonstrate that PPDM provides a practical and scalable solution for high-fidelity 3D diffusion-based medical image translation under limited computational resources.
We introduce TCAM-Diff, a novel 3D medical image generation model that reduces the memory requirements to encode and generate high-resolution 3D data. This model utilizes a decoder-only autoencoder method to learn triplane representation from dense volume and leverages generalization operations to prevent overfitting. Subsequently, it uses a triplane-aware cross-attention diffusion model to learn and integrate these features effectively. Furthermore, the features generated by the diffusion model can be rapidly transformed into 3D volumes using a pre-trained decoder module. Our experiments on three different scales of medical datasets, BrainTumour 128 x 128 x 128, Pancreas 256 x 256 x 256, and Colon 512 x 512 x 512, demonstrate outstanding results. We utilized MSE and SSIM to assess reconstruction quality and leveraged the Wasserstein Generative Adversarial Network (W-GAN) critic to assess generative quality. Comparisons with existing approaches show that our method gives better reconstruction and generation results than other encoder-decoder methods with similar-sized latent spaces.