Yılmaz Korkmaz

Yilmaz Korkmaz, Tolga Cukur, Vishal M. Patel

Magnetic Resonance Imaging (MRI) produces excellent soft tissue contrast, albeit it is an inherently slow imaging modality. Promising deep learning methods have recently been proposed to reconstruct accelerated MRI scans. However, existing methods still suffer from various limitations regarding image fidelity, contextual sensitivity, and reliance on fully-sampled acquisitions for model training. To comprehensively address these limitations, we propose a novel self-supervised deep reconstruction model, named Self-Supervised Diffusion Reconstruction (SSDiffRecon). SSDiffRecon expresses a conditional diffusion process as an unrolled architecture that interleaves cross-attention transformers for reverse diffusion steps with data-consistency blocks for physics-driven processing. Unlike recent diffusion methods for MRI reconstruction, a self-supervision strategy is adopted to train SSDiffRecon using only undersampled k-space data. Comprehensive experiments on public brain MR datasets demonstrates the superiority of SSDiffRecon against state-of-the-art supervised, and self-supervised baselines in terms of reconstruction speed and quality. Implementation will be available at https://github.com/yilmazkorkmaz1/SSDiffRecon.

Yilmaz Korkmaz, Vishal M. Patel

Magnetic Resonance Imaging (MRI) is one of the most important medical imaging modalities as it provides superior resolution of soft tissues, albeit with a notable limitation in scanning speed. The advent of deep learning has catalyzed the development of cutting-edge methods for the expedited reconstruction of MRI scans, utilizing convolutional neural networks and, more recently, vision transformers. Recently proposed structured state space models (e.g., Mamba) have gained some traction due to their efficiency and low computational requirements compared to transformer models. We propose an innovative MRI reconstruction framework that employs structured state space models at its core, aimed at amplifying both long-range contextual sensitivity and reconstruction efficacy. Comprehensive experiments on public brain MRI datasets show that our model sets new benchmarks beating state-of-the-art reconstruction baselines. Code will be available (https://github.com/yilmazkorkmaz1/MambaRecon).

Alper Güngör, Salman UH Dar, Şaban Öztürk et al.

Deep MRI reconstruction is commonly performed with conditional models that de-alias undersampled acquisitions to recover images consistent with fully-sampled data. Since conditional models are trained with knowledge of the imaging operator, they can show poor generalization across variable operators. Unconditional models instead learn generative image priors decoupled from the operator to improve reliability against domain shifts related to the imaging operator. Recent diffusion models are particularly promising given their high sample fidelity. Nevertheless, inference with a static image prior can perform suboptimally. Here we propose the first adaptive diffusion prior for MRI reconstruction, AdaDiff, to improve performance and reliability against domain shifts. AdaDiff leverages an efficient diffusion prior trained via adversarial mapping over large reverse diffusion steps. A two-phase reconstruction is executed following training: a rapid-diffusion phase that produces an initial reconstruction with the trained prior, and an adaptation phase that further refines the result by updating the prior to minimize data-consistency loss. Demonstrations on multi-contrast brain MRI clearly indicate that AdaDiff outperforms competing conditional and unconditional methods under domain shifts, and achieves superior or on par within-domain performance.

Yilmaz Korkmaz, Vishal M. Patel

Unpaired image-to-image translation is a challenging task due to the absence of paired examples, which complicates learning the complex mappings between the distinct distributions of the source and target domains. One of the most commonly used approach for this task is CycleGAN which requires the training of a new pair of generator-discriminator networks for each domain pair. In this paper, we propose a new image-to-image translation framework named Image-to-Image-Generative-Adversarial-CLIP (I2I-Galip) where we utilize a pre-trained multi-model foundation model (i.e., CLIP) to mitigate the need of separate generator-discriminator pairs for each source-target mapping while achieving better and more efficient multi-domain translation. By utilizing the massive knowledge gathered during pre-training a foundation model, our approach makes use of a single lightweight generator network with ~13M parameters for the multi-domain image translation task. Comprehensive experiments on translation performance in public MRI and CT datasets show the superior performance of the proposed framework over the existing approaches. Code will be available (https://github.com/yilmazkorkmaz1/I2I-Galip).

Yilmaz Korkmaz, Vishal M. Patel

MRI reconstruction is an inherently ill-posed inverse problem, since incomplete measurements admit many plausible solutions. This ambiguity becomes more severe under high acceleration, where pixel-domain continuous predictors tend to average over feasible reconstructions and suppress high-frequency anatomy. We address this limitation by moving reconstruction to discrete multi-scale latent space and posing it as autoregressive next-acceleration-scale prediction. Leveraging discrete priors proven effective in visual autoregressive modeling, our method restricts the solution to compact sequences of codebook tokens, enabling sharp reconstructions even from extremely sparse measurements. This discrete autoregressive formulation also aligns naturally with modern large language model post-training techniques. Building on this observation, we introduce on-policy privileged information distillation for visual autoregressive modeling, where a teacher is provided training only privileged context that is unavailable at inference, in our case fully sampled acquisitions, and supervises a student trained on its own rollouts, leading to consistent reconstruction gains. Through extensive experiments on the fastMRI benchmark, we show that our approach delivers improved reconstruction performance across diverse sampling patterns under extreme undersampling. Project website is \hyperlink{https://github.com/yilmazkorkmaz1/discrete-mri-reconstruction-opd}{here}.

Gokberk Elmas, Salman UH Dar, Yilmaz Korkmaz et al.

Multi-institutional efforts can facilitate training of deep MRI reconstruction models, albeit privacy risks arise during cross-site sharing of imaging data. Federated learning (FL) has recently been introduced to address privacy concerns by enabling distributed training without transfer of imaging data. Existing FL methods for MRI reconstruction employ conditional models to map from undersampled to fully-sampled acquisitions via explicit knowledge of the imaging operator. Since conditional models generalize poorly across different acceleration rates or sampling densities, imaging operators must be fixed between training and testing, and they are typically matched across sites. To improve generalization and flexibility in multi-institutional collaborations, here we introduce a novel method for MRI reconstruction based on Federated learning of Generative IMage Priors (FedGIMP). FedGIMP leverages a two-stage approach: cross-site learning of a generative MRI prior, and subject-specific injection of the imaging operator. The global MRI prior is learned via an unconditional adversarial model that synthesizes high-quality MR images based on latent variables. Specificity in the prior is preserved via a mapper subnetwork that produces site-specific latents. During inference, the prior is combined with subject-specific imaging operators to enable reconstruction, and further adapted to individual test samples by minimizing data-consistency loss. Comprehensive experiments on multi-institutional datasets clearly demonstrate enhanced generalization performance of FedGIMP against site-specific and federated methods based on conditional models, as well as traditional reconstruction methods.

Yilmaz Korkmaz, Salman UH Dar, Mahmut Yurt et al.

Supervised reconstruction models are characteristically trained on matched pairs of undersampled and fully-sampled data to capture an MRI prior, along with supervision regarding the imaging operator to enforce data consistency. To reduce supervision requirements, the recent deep image prior framework instead conjoins untrained MRI priors with the imaging operator during inference. Yet, canonical convolutional architectures are suboptimal in capturing long-range relationships, and priors based on randomly initialized networks may yield suboptimal performance. To address these limitations, here we introduce a novel unsupervised MRI reconstruction method based on zero-Shot Learned Adversarial TransformERs (SLATER). SLATER embodies a deep adversarial network with cross-attention transformers to map noise and latent variables onto coil-combined MR images. During pre-training, this unconditional network learns a high-quality MRI prior in an unsupervised generative modeling task. During inference, a zero-shot reconstruction is then performed by incorporating the imaging operator and optimizing the prior to maximize consistency to undersampled data. Comprehensive experiments on brain MRI datasets clearly demonstrate the superior performance of SLATER against state-of-the-art unsupervised methods.