A Systematic Benchmark of Intraoperative Ultrasound-to-MR Synthesis for Brain Tumour Surgery

Maximal safe resection is the primary objective in glioma surgery. Neuronavigation guidance is progressively degraded by brain shift after dural opening. Intraoperative MRI can compensate but needs dedicated infrastructure and is rarely available, whereas intraoperative ultrasound (ioUS) is inexpensive, repeatable, and compatible with routine workflows. Navigation systems combining ioUS with preoperative MRI usually rely on rigid registration; even deformable multimodal registration is limited by ultrasound speckle contrast, a narrow field of view, and the inability to represent structures absent from the preoperative scan, most critically the resection cavity and residual tumor. We propose an end-to-end pipeline that generates a new whole-brain MRI volume in the preoperative imaging space by merging the preoperative MRI, a synthetic MRI generated from the ioUS, and a deformable registration anchored on that synthetic image. It integrates a 2.5D residual-transformer synthesis backbone (ResViT-2.5D) and a two-stage registration coupling NiftyReg with a synthesis-anchored SynthMorph stage, operating directly on raw scanner inputs. On a post-resection ReMIND cohort, ResViT-2.5D produced synthetic images closely matching the intraoperative T2 across structural, intensity, and perceptual metrics. In 14 subjects with 215 expert landmarks, the synthesis-anchored registration reduced the mean target registration error from 6.27 to 5.86 mm, matching a strong classical NiftyReg baseline (5.85 mm) while yielding a diffeomorphic deformation field in every subject. The contribution is not a gain in registration accuracy but the integrated volume itself, which inside the ultrasound field of view it reflects the intraoperative post-resection state. This provides the surgeon with an MRI-like update of the operative field with potential for integration into surgical-navigation workflows.

Brain-MRI inpainting replaces a masked region of a scan with synthesized, anatomically plausible healthy tissue, so that analysis tools built for healthy brains can be applied to images they would otherwise reject. On the BraTS local-synthesis benchmark, which ranks submissions on the structural similarity index (SSIM), the peak signal-to-noise ratio, and the mean squared error (MSE) jointly, the strongest recent models are accurate, but several report blurry synthesized regions and attribute this to the mean-seeking behavior of the $\ell_1$ and MSE terms in their training losses. We address this in post-processing, forming a deep ensemble of the two co-first-place 2025 models and training a lightweight residual refiner on the ensemble's own outputs under an $\ell_1$ loss augmented with a structural-similarity term whose weight $λ$ we vary. At a moderate $λ$ the refiner improves SSIM over the ensemble, from $0.8767$ to $0.8780$ on a held-out reproduction of the official scorer and from $0.8555$ to $0.8572$ on the official validation leaderboard, with essentially no change in MSE. The gain is small but consistent, improving $62.6\%$ of the held-out cases with a signed-rank $p=2.2\times10^{-7}$, whereas over-weighting the structural term reverses it. Two ablations bound the effect. Adding any third model to the two-model ensemble degrades it, and classical unsharp masking fails to improve SSIM at any strength (best $0.8765$ against $0.8767$), so the gain reflects learned rather than indiscriminate sharpening. The result is a cheap, reproducible post-processing stage that improves an already strong ensemble without any large-scale retraining.

The ASNR-MICCAI BraTS Local Synthesis (Inpainting) task asks for the anatomically plausible completion of healthy brain tissue within a masked region of a T1-weighted MRI, providing a tumor-free anatomical reference for downstream analysis. As the task is scored by distortion metrics (SSIM, PSNR, MSE), we build a deterministic regression model and focus on giving it inductive biases tailored to inpainting. Our network follows the U-DiT principle of performing self-attention on a downsampled token grid: a volumetric encoder-decoder imports long-range context through a downsampled global self-attention block with three-dimensional rotary position embeddings, while convolutions and skip connections preserve high-frequency detail. Two ideas drive our results. First, we constrain the attention so that occluded ("void") tokens attend only to known-healthy tokens of the same volume, with a learned bias toward each query's contralateral homologue, forcing the completion to be inferred from observed anatomy rather than from other unknown regions. Second, we add a contralateral-symmetry input that supplies the mirrored healthy hemisphere as a patient-specific prior; since the brain is approximately bilaterally symmetric and lesions are typically unilateral, this prior improves the distortion metrics at matched structural similarity. On the official BraTS-2026 validation leaderboard our submission reaches a mean healthy-region SSIM of $0.864$, PSNR of $24.7$,dB and MSE of $4.6{\times}10^{-3}$ over $219$ cases. We further analyse the residual smoothness inherent to distortion-optimal regression and discuss its implications for anatomical realism.