Measure Before You Repair: An Explainable Agent for Blind Restoration of Multi-Artifact 3-D MRI

Patient motion remains a source of image degradation in brain MRI, leading to signal loss, blurring, and geometric distortion that compromise quantitative analysis. Existing deep learning methods for motion correction typically rely on paired clean-corrupted data or k-space acquisitions, which are rarely available in clinical settings. We propose SSRL-MAR, a motion artifact-aware unpaired representation learning framework for motion artifact reduction that requires neither paired training data nor explicit motion labels. SSRL-MAR employed a three-stage training strategy: (1) contrastive learning on 3D patches to extract motion representations by contrasting clean and synthetically corrupted images, (2) a motion artifact-aware synthesis network to generate motion artifacts from clean scans, and (3) a motion artifact-aware generator to restore clean volumes using the learned degrader for self-supervised supervision. On in-silico dataset, SSRL-MAR achieved PSNR 23.81dB, SSIM 91.55%, and NMSE 0.79%. On in-vivo MR-ART dataset, the pretrained model reduced motion distortion, and unsupervised domain adaptation further improved anatomical fidelity. Against a source-only supervised model trained on the same simulated pairs, SSRL-MAR improved PSNR by up to 2.0 dB on MR-ART after unsupervised domain adaptation, and remained within 0.25-0.47 dB of an oracle supervised model that requires real paired data unavailable in practice. At the milder motion level, volumetric error in structures such as the corpus callosum and ventricular system decreased by more than 50%, confirming improved neuroanatomical consistency. These results indicate that SSRL-MAR provides a robust and scalable image-domain solution for 3D brain MRI motion correction, enabling reliable structural quantification in large-scale neuroimaging studies without requiring prospectively acquired pairs or acquisition-specific calibration.

Medical image inpainting has the potential to improve automated brain MRI analysis by reconstructing healthy tissue within pathological regions. We introduce RARF, a task-agnostic region-aware rectified flow framework for masked data generation. We instantiate the framework for 3D brain MRI inpainting as our submission to the BraTS Inpainting Challenge 2026. RARF restricts the stochastic interpolation process to the inpainting region, while the observed voxels remain fixed and provide patient-specific anatomical context. A three-dimensional neural network receives the partially voided image, with Gaussian noise filling the missing region, together with the inpainting mask and the corresponding timestep. The model is trained using masked flow-matching and reconstruction-consistency objectives, combined with mask-aware preprocessing and data augmentation. During inference, the learned velocity field transports the initial noise toward a plausible reconstruction of the missing tissue, which is then combined with the unchanged observed anatomy. Experiments under the BraTS evaluation protocol show that the proposed approach produces competitive reconstructions while maintaining anatomical consistency. Source code is available at: https://github.com/TomasGuija/rarf.

Generative inpainting of brain MRI volumes is essential for synthesizing healthy tissue in pathological regions, improving the accuracy and reliability of automated downstream brain analysis applications such as image registration, brain extraction, and segmentation. However, standard 3D approaches are computationally prohibitive, while efficient 2D slice-wise methods suffer from severe inter-slice discontinuities. Furthermore, traditional models rely on conditional training, requiring task-specific learning of masked inputs. We propose a zero-shot brain MRI inpainting framework utilizing 2.5D unconditional flow priors to capture spatial context along the superior-inferior axis without the overhead of full 3D convolutions. During training, our flow matching model learns the joint distribution of adjacent axial slice triplets, modeling the manifold of healthy brain anatomy while explicitly excluding pathological regions from the loss function. At inference, the model processes the input triplets autoregressively along the depth axis. We employ the Restora-Flow solver to constrain the unconditional prior using the input mask, achieving accurate zero-shot inpainting. Evaluations show our 2.5D strategy resolves the structural discontinuities of 2D baselines, synthesizing plausible healthy tissue while maintaining volumetric consistency across the axial, sagittal, and coronal planes. As a final step, we generate and average an ensemble of multiple stochastic reconstructions to form the final prediction. Quantitative results benchmarked on the official BraTS 2026 Inpainting Challenge validation set demonstrate the effectiveness of our proposed approach, yielding an SSIM of 0.816 $\pm$ 0.112, MSE of 0.007 $\pm$ 0.005, and PSNR of 22.923 $\pm$ 4.343. Code is available at https://github.com/imigraz/brats2026-inpainting.