An Adaptive Attention 3D U-Net for High-Fidelity MRI-to-CT Synthesis: Bridging the Anatomical Gap with CBAM

Background: The generation of synthetic CT images from MRI scans represents a crucial step toward enabling MRI-only clinical workflows and supporting multi-modal integration in medical imaging, particularly in radiotherapy planning. Despite significant advancements in deep learning models, many current methods still struggle to reconstruct high-density structures, especially bone, and exhibit limited accuracy in density values. This shortcoming is largely attributed to the passage of excessive or noisy features through skip connections in the traditional U-Net architecture, which degrade the quality of information transmitted to the decoder, negatively impacting the clarity of anatomical boundaries and the pixel-wise accuracy of the resulting synthetic image. Methods: In this work, we propose an enhanced 3D U-Net architecture in which the Convolutional Block Attention Module (CBAM) is systematically integrated within each skip connection. The CBAM sequentially applies channel and spatial attention to adaptively reweight encoder feature maps before fusion with the decoder, thereby emphasizing anatomically relevant structures while suppressing irrelevant feature propagation. The model was trained and evaluated on the SynthRAD2023 (Task 1—Brain) MRI–CT dataset. To rigorously assess the contribution of the attention mechanism, a dedicated ablation study was conducted comparing three variants: 3D U-Net with Squeeze-and-Excitation (SE), Coordinate Attention (CA), and the proposed CBAM module. Performance was evaluated using Mean Absolute Error (MAE), Root Mean Square Error (RMSE), Peak Signal-to-Noise Ratio (PSNR), Structural Similarity Index (SSIM), and Normalized Cross-Correlation (NCC). Results: The ablation study demonstrated that the CBAM-enhanced model consistently outperformed both SE- and CA-based variants across all quantitative metrics. Specifically, the proposed method achieved an MAE of 38.2±5.4 HU and an RMSE of 51.0±12.0 HU, representing the lowest reconstruction errors among the evaluated models. In addition, it obtained a PSNR of 29.45±2.10 dB, SSIM of 0.940±0.031, and NCC of 0.967±0.015, indicating superior structural preservation and strong voxel-wise correspondence between synthesized and reference CT volumes. These results confirm that the sequential integration of channel and spatial attention provides a statistically and practically meaningful improvement for high-fidelity MRI-to-CT synthesis. Discussion and Conclusions: Generating high-resolution brain CT images from brain MRI scans using a 3D U-Net network enhanced with a CBAM module can contribute to supporting the clinical workflow by providing additional diagnostic data without the need for extra radiological examinations, thereby enhancing diagnostic efficiency and reducing radiation exposure. This technique helps reduce patient exposure to radiation and improves accessibility in resource-limited settings. Furthermore, this method is valuable for retrospective studies, surgical planning, and image-guided therapy, where complete multi-modal data may not always be available.