Mehmet Akçakaya

Kerstin Hammernik, Thomas Küstner, Burhaneddin Yaman et al.

Physics-driven deep learning methods have emerged as a powerful tool for computational magnetic resonance imaging (MRI) problems, pushing reconstruction performance to new limits. This article provides an overview of the recent developments in incorporating physics information into learning-based MRI reconstruction. We consider inverse problems with both linear and non-linear forward models for computational MRI, and review the classical approaches for solving these. We then focus on physics-driven deep learning approaches, covering physics-driven loss functions, plug-and-play methods, generative models, and unrolled networks. We highlight domain-specific challenges such as real- and complex-valued building blocks of neural networks, and translational applications in MRI with linear and non-linear forward models. Finally, we discuss common issues and open challenges, and draw connections to the importance of physics-driven learning when combined with other downstream tasks in the medical imaging pipeline.

Yaşar Utku Alçalar, Mehmet Akçakaya

Diffusion models have emerged as powerful generative techniques for solving inverse problems. Despite their success in a variety of inverse problems in imaging, these models require many steps to converge, leading to slow inference time. Recently, there has been a trend in diffusion models for employing sophisticated noise schedules that involve more frequent iterations of timesteps at lower noise levels, thereby improving image generation and convergence speed. However, application of these ideas for solving inverse problems with diffusion models remain challenging, as these noise schedules do not perform well when using empirical tuning for the forward model log-likelihood term weights. To tackle these challenges, we propose zero-shot approximate posterior sampling (ZAPS) that leverages connections to zero-shot physics-driven deep learning. ZAPS fixes the number of sampling steps, and uses zero-shot training with a physics-guided loss function to learn log-likelihood weights at each irregular timestep. We apply ZAPS to the recently proposed diffusion posterior sampling method as baseline, though ZAPS can also be used with other posterior sampling diffusion models. We further approximate the Hessian of the logarithm of the prior using a diagonalization approach with learnable diagonal entries for computational efficiency. These parameters are optimized over a fixed number of epochs with a given computational budget. Our results for various noisy inverse problems, including Gaussian and motion deblurring, inpainting, and super-resolution show that ZAPS reduces inference time, provides robustness to irregular noise schedules and improves reconstruction quality. Code is available at https://github.com/ualcalar17/ZAPS

Hongyi Gu, Burhaneddin Yaman, Steen Moeller et al.

Recent studies show that deep learning (DL) based MRI reconstruction outperforms conventional methods, such as parallel imaging and compressed sensing (CS), in multiple applications. Unlike CS that is typically implemented with pre-determined linear representations for regularization, DL inherently uses a non-linear representation learned from a large database. Another line of work uses transform learning (TL) to bridge the gap between these two approaches by learning linear representations from data. In this work, we combine ideas from CS, TL and DL reconstructions to learn deep linear convolutional transforms as part of an algorithm unrolling approach. Using end-to-end training, our results show that the proposed technique can reconstruct MR images to a level comparable to DL methods, while supporting uniform undersampling patterns unlike conventional CS methods. Our proposed method relies on convex sparse image reconstruction with linear representation at inference time, which may be beneficial for characterizing robustness, stability and generalizability.

Burhaneddin Yaman, Seyed Amir Hossein Hosseini, Mehmet Akçakaya

Deep learning (DL) has emerged as a powerful tool for accelerated MRI reconstruction, but often necessitates a database of fully-sampled measurements for training. Recent self-supervised and unsupervised learning approaches enable training without fully-sampled data. However, a database of undersampled measurements may not be available in many scenarios, especially for scans involving contrast or translational acquisitions in development. Moreover, recent studies show that database-trained models may not generalize well when the unseen measurements differ in terms of sampling pattern, acceleration rate, SNR, image contrast, and anatomy. Such challenges necessitate a new methodology to enable subject-specific DL MRI reconstruction without external training datasets, since it is clinically imperative to provide high-quality reconstructions that can be used to identify lesions/disease for \emph{every individual}. In this work, we propose a zero-shot self-supervised learning approach to perform subject-specific accelerated DL MRI reconstruction to tackle these issues. The proposed approach partitions the available measurements from a single scan into three disjoint sets. Two of these sets are used to enforce data consistency and define loss during training for self-supervision, while the last set serves to self-validate, establishing an early stopping criterion. In the presence of models pre-trained on a database with different image characteristics, we show that the proposed approach can be combined with transfer learning for faster convergence time and reduced computational complexity. The code is available at \url{https://github.com/byaman14/ZS-SSL}.

Yaşar Utku Alçalar, Mehmet Akçakaya

Physics-driven deep learning (PD-DL) models have proven to be a powerful approach for improved reconstruction of rapid MRI scans. In order to train these models in scenarios where fully-sampled reference data is unavailable, self-supervised learning has gained prominence. However, its application at high acceleration rates frequently introduces artifacts, compromising image fidelity. To mitigate this shortcoming, we propose a novel way to train PD-DL networks via carefully-designed perturbations. In particular, we enhance the k-space masking idea of conventional self-supervised learning with a novel consistency term that assesses the model's ability to accurately predict the added perturbations in a sparse domain, leading to more reliable and artifact-free reconstructions. The results obtained from the fastMRI knee and brain datasets show that the proposed training strategy effectively reduces aliasing artifacts and mitigates noise amplification at high acceleration rates, outperforming state-of-the-art self-supervised methods both visually and quantitatively.

Merve Gülle, Junno Yun, Yaşar Utku Alçalar et al.

Diffusion models have found extensive use in solving numerous inverse problems. Such diffusion inverse problem solvers aim to sample from the posterior distribution of data given the measurements, using a combination of the unconditional score function and an approximation of the posterior related to the forward process. Recently, consistency models (CMs) have been proposed to directly predict the final output from any point on the diffusion ODE trajectory, enabling high-quality sampling in just a few NFEs. CMs have also been utilized for inverse problems, but existing CM-based solvers either require additional task-specific training or utilize data fidelity operations with slow convergence, not amenable to large-scale problems. In this work, we reinterpret CMs as proximal operators of a prior, enabling their integration into plug-and-play (PnP) frameworks. We propose a solver based on PnP-ADMM, which enables us to leverage the fast convergence of conjugate gradient method. We further accelerate this with noise injection and momentum, dubbed PnP-CM, and show it maintains the convergence properties of the baseline PnP-ADMM. We evaluate our approach on a variety of inverse problems, including inpainting, super-resolution, Gaussian deblurring, and magnetic resonance imaging (MRI) reconstruction. To the best of our knowledge, this is the first CM trained for MRI datasets. Our results show that PnP-CM achieves high-quality reconstructions in as few as 4 NFEs, and can produce meaningful results in 2 steps, highlighting its effectiveness in real-world inverse problems while outperforming comparable CM-based approaches.

Yaşar Utku Alçalar, Junno Yun, Mehmet Akçakaya

Diffusion/score-based models have recently emerged as powerful generative priors for solving inverse problems, including accelerated MRI reconstruction. While their flexibility allows decoupling the measurement model from the learned prior, their performance heavily depends on carefully tuned data fidelity weights, especially under fast sampling schedules with few denoising steps. Existing approaches often rely on heuristics or fixed weights, which fail to generalize across varying measurement conditions and irregular timestep schedules. In this work, we propose Zero-shot Adaptive Diffusion Sampling (ZADS), a test-time optimization method that adaptively tunes fidelity weights across arbitrary noise schedules without requiring retraining of the diffusion prior. ZADS treats the denoising process as a fixed unrolled sampler and optimizes fidelity weights in a self-supervised manner using only undersampled measurements. Experiments on the fastMRI knee dataset demonstrate that ZADS consistently outperforms both traditional compressed sensing and recent diffusion-based methods, showcasing its ability to deliver high-fidelity reconstructions across varying noise schedules and acquisition settings.

Hongyi Gu, Chi Zhang, Zidan Yu et al.

Functional MRI (fMRI) is an important tool for non-invasive studies of brain function. Over the past decade, multi-echo fMRI methods that sample multiple echo times has become popular with potential to improve quantification. While these acquisitions are typically performed with Cartesian trajectories, non-Cartesian trajectories, in particular spiral acquisitions, hold promise for denser sampling of echo times. However, such acquisitions require very high acceleration rates for sufficient spatiotemporal resolutions. In this work, we propose to use a physics-driven deep learning (PD-DL) reconstruction to accelerate multi-echo spiral fMRI by 10-fold. We modify a self-supervised learning algorithm for optimized training with non-Cartesian trajectories and use it to train the PD-DL network. Results show that the proposed self-supervised PD-DL reconstruction achieves high spatio-temporal resolution with meaningful BOLD analysis.

Junno Yun, Yaşar Utku Alçalar, Mehmet Akçakaya

Algorithm unrolling methods have proven powerful for solving the regularized least squares problem in computational magnetic resonance imaging (MRI). These approaches unfold an iterative algorithm with a fixed number of iterations, typically alternating between a neural network-based proximal operator for regularization, a data fidelity operation and auxiliary updates with learnable parameters. While the connection to optimization methods dictate that the proximal operator network should be shared across unrolls, this can introduce artifacts or blurring. Heuristically, practitioners have shown that using distinct networks may be beneficial, but this significantly increases the number of learnable parameters, making it challenging to prevent overfitting. To address these shortcomings, by taking inspirations from proximal operators with varying thresholds in approximate message passing (AMP) and the success of time-embedding in diffusion models, we propose a time-embedded algorithm unrolling scheme for inverse problems. Specifically, we introduce a novel perspective on the iteration-dependent proximal operation in vector AMP (VAMP) and the subsequent Onsager correction in the context of algorithm unrolling, framing them as a time-embedded neural network. Similarly, the scalar weights in the data fidelity operation and its associated Onsager correction are cast as time-dependent learnable parameters. Our extensive experiments on the fastMRI dataset, spanning various acceleration rates and datasets, demonstrate that our method effectively reduces aliasing artifacts and mitigates noise amplification, achieving state-of-the-art performance. Furthermore, we show that our time-embedding strategy extends to existing algorithm unrolling approaches, enhancing reconstruction quality without increasing the computational complexity significantly.

Mahdi Saberi, Chi Zhang, Mehmet Akçakaya

Deep learning (DL) methods have become the state-of-the-art for reconstructing sub-sampled magnetic resonance imaging (MRI) data. However, studies have shown that these methods are susceptible to small adversarial input perturbations, or attacks, resulting in major distortions in the output images. Various strategies have been proposed to reduce the effects of these attacks, but they require retraining and may lower reconstruction quality for non-perturbed/clean inputs. In this work, we propose a novel approach for mitigating adversarial attacks on MRI reconstruction models without any retraining. Based on the idea of cyclic measurement consistency, we devise a novel mitigation objective that is minimized in a small ball around the attack input. Results show that our method substantially reduces the impact of adversarial perturbations across different datasets, attack types/strengths and PD-DL networks, and qualitatively and quantitatively outperforms conventional mitigation methods that involve retraining. We also introduce a practically relevant scenario for small adversarial perturbations that models impulse noise in raw data, which relates to \emph{herringbone artifacts}, and show the applicability of our approach in this setting. Finally, we show our mitigation approach remains effective in two \emph{realistic} extension scenarios: a blind setup, where the attack strength or algorithm is not known to the user; and an adaptive attack setup, where the attacker has full knowledge of the defense strategy.

Yaşar Utku Alçalar, Merve Gülle, Mehmet Akçakaya

Physics-driven deep learning (PD-DL) approaches have become popular for improved reconstruction of fast magnetic resonance imaging (MRI) scans. Though PD-DL offers higher acceleration rates than existing clinical fast MRI techniques, their use has been limited outside specialized MRI centers. A key challenge is generalization to rare pathologies or different populations, noted in multiple studies, with fine-tuning on target populations suggested for improvement. However, current approaches for PD-DL training require access to raw k-space measurements, which is typically only available at specialized MRI centers that have research agreements for such data access. This is especially an issue for rural and under-resourced areas, where commercial MRI scanners only provide access to a final reconstructed image. To tackle these challenges, we propose Compressibility-inspired Unsupervised Learning via Parallel Imaging Fidelity (CUPID) for high-quality PD-DL training using only routine clinical reconstructed images exported from an MRI scanner. CUPID evaluates output quality with a compressibility-based approach while ensuring that the output stays consistent with the clinical parallel imaging reconstruction through well-designed perturbations. Our results show CUPID achieves similar quality to established PD-DL training that requires k-space data while outperforming compressed sensing (CS) and diffusion-based generative methods. We further demonstrate its effectiveness in a zero-shot training setup for retrospectively and prospectively sub-sampled acquisitions, attesting to its minimal training burden. As an approach that radically deviates from existing strategies, CUPID presents an opportunity to provide broader access to fast MRI for remote and rural populations in an attempt to reduce the obstacles associated with this expensive imaging modality.

Junno Yun, Yaşar Utku Alçalar, Mehmet Akçakaya

Efficient training strategies for large-scale diffusion models have recently emphasized the importance of improving discriminative feature representations in these models. A central line of work in this direction is representation alignment with features obtained from powerful external encoders, which improves the representation quality as assessed through linear probing. Alignment-based approaches show promise but depend on large pretrained encoders, which are computationally expensive to obtain. In this work, we propose an alternative regularization for training, based on promoting the Linear SEParability (LSEP) of intermediate layer representations. LSEP eliminates the need for an auxiliary encoder and representation alignment, while incorporating linear probing directly into the network's learning dynamics rather than treating it as a simple post-hoc evaluation tool. Our results demonstrate substantial improvements in both training efficiency and generation quality on flow-based transformer architectures such as SiTs, achieving an FID of 1.46 on $256 \times 256$ ImageNet dataset.

Jarvis Haupt, Qin Lu, Yanning Shen et al.

Powerful artificial intelligence (AI) tools that have emerged in recent years -- including large language models, automated coding assistants, and advanced image and speech generation technologies -- are the result of monumental human achievements. These breakthroughs reflect mastery across multiple technical disciplines and the resolution of significant technological challenges. However, some of the most profound challenges may still lie ahead. These challenges are not purely technical but pertain to the fair and responsible use of AI in ways that genuinely improve the global human condition. This article explores one promising application aligned with that vision: the use of AI tools to facilitate and enhance education, with a specific focus on signal processing (SP). It presents two interrelated perspectives: identifying and addressing technical limitations, and applying AI tools in practice to improve educational experiences. Primers are provided on several core technical issues that arise when using AI in educational settings, including how to ensure fairness and inclusivity, handle hallucinated outputs, and achieve efficient use of resources. These and other considerations -- such as transparency, explainability, and trustworthiness -- are illustrated through the development of an immersive, structured, and reliable "smart textbook." The article serves as a resource for researchers and educators seeking to advance AI's role in engineering education.

Yaşar Utku Alçalar, Yu Cao, Mehmet Akçakaya

Physics-driven artificial intelligence (PD-AI) reconstruction methods have emerged as the state-of-the-art for accelerating MRI scans, enabling higher spatial and temporal resolutions. However, the high resolution of these scans generates massive data volumes, leading to challenges in transmission, storage, and real-time processing. This is particularly pronounced in functional MRI, where hundreds of volumetric acquisitions further exacerbate these demands. Edge computing with FPGAs presents a promising solution for enabling PD-AI reconstruction near the MRI sensors, reducing data transfer and storage bottlenecks. However, this requires optimization of PD-AI models for hardware efficiency through quantization and bypassing traditional FFT-based approaches, which can be a limitation due to their computational demands. In this work, we propose a novel PD-AI computational MRI approach optimized for FPGA-based edge computing devices, leveraging 8-bit complex data quantization and eliminating redundant FFT/IFFT operations. Our results show that this strategy improves computational efficiency while maintaining reconstruction quality comparable to conventional PD-AI methods, and outperforms standard clinical methods. Our approach presents an opportunity for high-resolution MRI reconstruction on resource-constrained devices, highlighting its potential for real-world deployment.

Merve Gülle, Sebastian Weingärtner, Mehmet Akçakaya

Real-time (RT) dynamic MRI plays a vital role in capturing rapid physiological processes, offering unique insights into organ motion and function. Among these applications, RT cine MRI is particularly important for functional assessment of the heart with high temporal resolution. RT imaging enables free-breathing, ungated imaging of cardiac motion, making it a crucial alternative for patients who cannot tolerate conventional breath-hold, ECG-gated acquisitions. However, achieving high acceleration rates in RT cine MRI is challenging due to aliasing artifacts from extra-cardiac tissues, particularly at high undersampling factors. In this study, we propose a novel outer volume removal (OVR) method to address this challenge by eliminating aliasing contributions from non-cardiac regions in a post-processing framework. Our approach estimates the outer volume signal for each timeframe using composite temporal images from time-interleaved undersampling patterns, which inherently contain pseudo-periodic ghosting artifacts. A deep learning (DL) model is trained to identify and remove these artifacts, producing a clean outer volume estimate that is subsequently subtracted from the corresponding k-space data. The final reconstruction is performed with a physics-driven DL (PD-DL) method trained using an OVR-specific loss function to restore high spatio-temporal resolution images. Experimental results show that the proposed method at high accelerations achieves image quality that is visually comparable to clinical baseline images, while outperforming conventional reconstruction techniques, both qualitatively and quantitatively. The proposed approach provides a practical and effective solution for artifact reduction in RT cine MRI without requiring acquisition modifications, offering a pathway to higher acceleration rates while preserving diagnostic quality.

Junno Yun, Mehmet Akçakaya

Infrared (IR) imaging is commonly used in various scenarios, including autonomous driving, fire safety and defense applications. Thus, semantic segmentation of such images is of great interest. However, this task faces several challenges, including data scarcity, differing contrast and input channel number compared to natural images, and emergence of classes not represented in databases in certain scenarios, such as defense applications. Few-shot segmentation (FSS) provides a framework to overcome these issues by segmenting query images using a few labeled support samples. However, existing FSS models for IR images require paired visible RGB images, which is a major limitation since acquiring such paired data is difficult or impossible in some applications. In this work, we develop new strategies for FSS of IR images by using generative modeling and fusion techniques. To this end, we propose to synthesize auxiliary data to provide additional channel information to complement the limited contrast in the IR images, as well as IR data synthesis for data augmentation. Here, the former helps the FSS model to better capture the relationship between the support and query sets, while the latter addresses the issue of data scarcity. Finally, to further improve the former aspect, we propose a novel fusion ensemble module for integrating the two different modalities. Our methods are evaluated on different IR datasets, and improve upon the state-of-the-art (SOTA) FSS models.

Mehmet Akçakaya, Burhaneddin Yaman, Hyungjin Chung et al.

Recently, deep learning approaches have become the main research frontier for biological image reconstruction and enhancement problems thanks to their high performance, along with their ultra-fast inference times. However, due to the difficulty of obtaining matched reference data for supervised learning, there has been increasing interest in unsupervised learning approaches that do not need paired reference data. In particular, self-supervised learning and generative models have been successfully used for various biological imaging applications. In this paper, we overview these approaches from a coherent perspective in the context of classical inverse problems, and discuss their applications to biological imaging, including electron, fluorescence and deconvolution microscopy, optical diffraction tomography and functional neuroimaging.

Omer Burak Demirel, Burhaneddin Yaman, Logan Dowdle et al.

High spatial and temporal resolution across the whole brain is essential to accurately resolve neural activities in fMRI. Therefore, accelerated imaging techniques target improved coverage with high spatio-temporal resolution. Simultaneous multi-slice (SMS) imaging combined with in-plane acceleration are used in large studies that involve ultrahigh field fMRI, such as the Human Connectome Project. However, for even higher acceleration rates, these methods cannot be reliably utilized due to aliasing and noise artifacts. Deep learning (DL) reconstruction techniques have recently gained substantial interest for improving highly-accelerated MRI. Supervised learning of DL reconstructions generally requires fully-sampled training datasets, which is not available for high-resolution fMRI studies. To tackle this challenge, self-supervised learning has been proposed for training of DL reconstruction with only undersampled datasets, showing similar performance to supervised learning. In this study, we utilize a self-supervised physics-guided DL reconstruction on a 5-fold SMS and 4-fold in-plane accelerated 7T fMRI data. Our results show that our self-supervised DL reconstruction produce high-quality images at this 20-fold acceleration, substantially improving on existing methods, while showing similar functional precision and temporal effects in the subsequent analysis compared to a standard 10-fold accelerated acquisition.

Omer Burak Demirel, Burhaneddin Yaman, Logan Dowdle et al.

Functional MRI (fMRI) is commonly used for interpreting neural activities across the brain. Numerous accelerated fMRI techniques aim to provide improved spatiotemporal resolutions. Among these, simultaneous multi-slice (SMS) imaging has emerged as a powerful strategy, becoming a part of large-scale studies, such as the Human Connectome Project. However, when SMS imaging is combined with in-plane acceleration for higher acceleration rates, conventional SMS reconstruction methods may suffer from noise amplification and other artifacts. Recently, deep learning (DL) techniques have gained interest for improving MRI reconstruction. However, these methods are typically trained in a supervised manner that necessitates fully-sampled reference data, which is not feasible in highly-accelerated fMRI acquisitions. Self-supervised learning that does not require fully-sampled data has recently been proposed and has shown similar performance to supervised learning. However, it has only been applied for in-plane acceleration. Furthermore the effect of DL reconstruction on subsequent fMRI analysis remains unclear. In this work, we extend self-supervised DL reconstruction to SMS imaging. Our results on prospectively 10-fold accelerated 7T fMRI data show that self-supervised DL reduces reconstruction noise and suppresses residual artifacts. Subsequent fMRI analysis remains unaltered by DL processing, while the improved temporal signal-to-noise ratio produces higher coherence estimates between task runs.

Chi Zhang, Jinghan Jia, Burhaneddin Yaman et al.

Although deep learning (DL) has received much attention in accelerated MRI, recent studies suggest small perturbations may lead to instabilities in DL-based reconstructions, leading to concern for their clinical application. However, these works focus on single-coil acquisitions, which is not practical. We investigate instabilities caused by small adversarial attacks for multi-coil acquisitions. Our results suggest that, parallel imaging and multi-coil CS exhibit considerable instabilities against small adversarial perturbations.

Burhaneddin Yaman, Chetan Shenoy, Zilin Deng et al.

Late gadolinium enhancement (LGE) cardiac MRI (CMR) is the clinical standard for diagnosis of myocardial scar. 3D isotropic LGE CMR provides improved coverage and resolution compared to 2D imaging. However, image acceleration is required due to long scan times and contrast washout. Physics-guided deep learning (PG-DL) approaches have recently emerged as an improved accelerated MRI strategy. Training of PG-DL methods is typically performed in supervised manner requiring fully-sampled data as reference, which is challenging in 3D LGE CMR. Recently, a self-supervised learning approach was proposed to enable training PG-DL techniques without fully-sampled data. In this work, we extend this self-supervised learning approach to 3D imaging, while tackling challenges related to small training database sizes of 3D volumes. Results and a reader study on prospectively accelerated 3D LGE show that the proposed approach at 6-fold acceleration outperforms the clinically utilized compressed sensing approach at 3-fold acceleration.

Burhaneddin Yaman, Seyed Amir Hossein Hosseini, Steen Moeller et al.

Physics-guided deep learning (PG-DL) via algorithm unrolling has received significant interest for improved image reconstruction, including MRI applications. These methods unroll an iterative optimization algorithm into a series of regularizer and data consistency units. The unrolled networks are typically trained end-to-end using a supervised approach. Current supervised PG-DL approaches use all of the available sub-sampled measurements in their data consistency units. Thus, the network learns to fit the rest of the measurements. In this study, we propose to improve the performance and robustness of supervised training by utilizing randomness by retrospectively selecting only a subset of all the available measurements for data consistency units. The process is repeated multiple times using different random masks during training for further enhancement. Results on knee MRI show that the proposed multi-mask supervised PG-DL enhances reconstruction performance compared to conventional supervised PG-DL approaches.

Burhaneddin Yaman, Hongyi Gu, Seyed Amir Hossein Hosseini et al.

Self-supervised learning has shown great promise due to its capability to train deep learning MRI reconstruction methods without fully-sampled data. Current self-supervised learning methods for physics-guided reconstruction networks split acquired undersampled data into two disjoint sets, where one is used for data consistency (DC) in the unrolled network and the other to define the training loss. In this study, we propose an improved self-supervised learning strategy that more efficiently uses the acquired data to train a physics-guided reconstruction network without a database of fully-sampled data. The proposed multi-mask self-supervised learning via data undersampling (SSDU) applies a hold-out masking operation on acquired measurements to split it into multiple pairs of disjoint sets for each training sample, while using one of these pairs for DC units and the other for defining loss, thereby more efficiently using the undersampled data. Multi-mask SSDU is applied on fully-sampled 3D knee and prospectively undersampled 3D brain MRI datasets, for various acceleration rates and patterns, and compared to CG-SENSE and single-mask SSDU DL-MRI, as well as supervised DL-MRI when fully-sampled data is available. Results on knee MRI show that the proposed multi-mask SSDU outperforms SSDU and performs closely with supervised DL-MRI. A clinical reader study further ranks the multi-mask SSDU higher than supervised DL-MRI in terms of SNR and aliasing artifacts. Results on brain MRI show that multi-mask SSDU achieves better reconstruction quality compared to SSDU. Reader study demonstrates that multi-mask SSDU at R=8 significantly improves reconstruction compared to single-mask SSDU at R=8, as well as CG-SENSE at R=2.

Burhaneddin Yaman, Seyed Amir Hossein Hosseini, Mehmet Akçakaya

Deep learning based image denoising methods have been recently popular due to their improved performance. Traditionally, these methods are trained in a supervised manner, requiring a set of noisy input and clean target image pairs. More recently, self-supervised approaches have been proposed to learn denoising from only noisy images. These methods assume that noise across pixels is statistically independent, and the underlying image pixels show spatial correlations across neighborhoods. These methods rely on a masking approach that divides the image pixels into two disjoint sets, where one is used as input to the network while the other is used to define the loss. However, these previous self-supervised approaches rely on a purely data-driven regularization neural network without explicitly taking the masking model into account. In this work, building on these self-supervised approaches, we introduce Noise2Inpaint (N2I), a training approach that recasts the denoising problem into a regularized image inpainting framework. This allows us to use an objective function, which can incorporate different statistical properties of the noise as needed. We use algorithm unrolling to unroll an iterative optimization for solving this objective function and train the unrolled network end-to-end. The training paradigm follows the masking approach from previous works, splitting the pixels into two disjoint sets. Importantly, one of these is now used to impose data fidelity in the unrolled network, while the other still defines the loss. We demonstrate that N2I performs successful denoising on real-world datasets, while better preserving details compared to its purely data-driven counterpart Noise2Self.

Seyed Amir Hossein Hosseini, Burhaneddin Yaman, Steen Moeller et al.

Long scan duration remains a challenge for high-resolution MRI. Deep learning has emerged as a powerful means for accelerated MRI reconstruction by providing data-driven regularizers that are directly learned from data. These data-driven priors typically remain unchanged for future data in the testing phase once they are learned during training. In this study, we propose to use a transfer learning approach to fine-tune these regularizers for new subjects using a self-supervision approach. While the proposed approach can compromise the extremely fast reconstruction time of deep learning MRI methods, our results on knee MRI indicate that such adaptation can substantially reduce the remaining artifacts in reconstructed images. In addition, the proposed approach has the potential to reduce the risks of generalization to rare pathological conditions, which may be unavailable in the training data.

Burhaneddin Yaman, Seyed Amir Hossein Hosseini, Steen Moeller et al.

Purpose: To develop a strategy for training a physics-guided MRI reconstruction neural network without a database of fully-sampled datasets. Theory and Methods: Self-supervised learning via data under-sampling (SSDU) for physics-guided deep learning (DL) reconstruction partitions available measurements into two disjoint sets, one of which is used in the data consistency units in the unrolled network and the other is used to define the loss for training. The proposed training without fully-sampled data is compared to fully-supervised training with ground-truth data, as well as conventional compressed sensing and parallel imaging methods using the publicly available fastMRI knee database. The same physics-guided neural network is used for both proposed SSDU and supervised training. The SSDU training is also applied to prospectively 2-fold accelerated high-resolution brain datasets at different acceleration rates, and compared to parallel imaging. Results: Results on five different knee sequences at acceleration rate of 4 shows that proposed self-supervised approach performs closely with supervised learning, while significantly outperforming conventional compressed sensing and parallel imaging, as characterized by quantitative metrics and a clinical reader study. The results on prospectively sub-sampled brain datasets, where supervised learning cannot be employed due to lack of ground-truth reference, show that the proposed self-supervised approach successfully perform reconstruction at high acceleration rates (4, 6 and 8). Image readings indicate improved visual reconstruction quality with the proposed approach compared to parallel imaging at acquisition acceleration. Conclusion: The proposed SSDU approach allows training of physics-guided DL-MRI reconstruction without fully-sampled data, while achieving comparable results with supervised DL-MRI trained on fully-sampled data.

Seyed Amir Hossein Hosseini, Burhaneddin Yaman, Steen Moeller et al.

Inverse problems for accelerated MRI typically incorporate domain-specific knowledge about the forward encoding operator in a regularized reconstruction framework. Recently physics-driven deep learning (DL) methods have been proposed to use neural networks for data-driven regularization. These methods unroll iterative optimization algorithms to solve the inverse problem objective function, by alternating between domain-specific data consistency and data-driven regularization via neural networks. The whole unrolled network is then trained end-to-end to learn the parameters of the network. Due to simplicity of data consistency updates with gradient descent steps, proximal gradient descent (PGD) is a common approach to unroll physics-driven DL reconstruction methods. However, PGD methods have slow convergence rates, necessitating a higher number of unrolled iterations, leading to memory issues in training and slower reconstruction times in testing. Inspired by efficient variants of PGD methods that use a history of the previous iterates, we propose a history-cognizant unrolling of the optimization algorithm with dense connections across iterations for improved performance. In our approach, the gradient descent steps are calculated at a trainable combination of the outputs of all the previous regularization units. We also apply this idea to unrolling variable splitting methods with quadratic relaxation. Our results in reconstruction of the fastMRI knee dataset show that the proposed history-cognizant approach reduces residual aliasing artifacts compared to its conventional unrolled counterpart without requiring extra computational power or increasing reconstruction time.

Burhaneddin Yaman, Seyed Amir Hossein Hosseini, Steen Moeller et al.

Deep learning (DL) has emerged as a tool for improving accelerated MRI reconstruction. A common strategy among DL methods is the physics-based approach, where a regularized iterative algorithm alternating between data consistency and a regularizer is unrolled for a finite number of iterations. This unrolled network is then trained end-to-end in a supervised manner, using fully-sampled data as ground truth for the network output. However, in a number of scenarios, it is difficult to obtain fully-sampled datasets, due to physiological constraints such as organ motion or physical constraints such as signal decay. In this work, we tackle this issue and propose a self-supervised learning strategy that enables physics-based DL reconstruction without fully-sampled data. Our approach is to divide the acquired sub-sampled points for each scan into training and validation subsets. During training, data consistency is enforced over the training subset, while the validation subset is used to define the loss function. Results show that the proposed self-supervised learning method successfully reconstructs images without fully-sampled data, performing similarly to the supervised approach that is trained with fully-sampled references. This has implications for physics-based inverse problem approaches for other settings, where fully-sampled data is not available or possible to acquire.