Mathews Jacob

Yan Chen, James H. Holmes, Curtis Corum et al.

Recent quantitative parameter mapping methods including MR fingerprinting (MRF) collect a time series of images that capture the evolution of magnetization. The focus of this work is to introduce a novel approach termed as Deep Factor Model(DFM), which offers an efficient representation of the multi-contrast image time series. The higher efficiency of the representation enables the acquisition of the images in a highly undersampled fashion, which translates to reduced scan time in 3D high-resolution multi-contrast applications. The approach integrates motion estimation and compensation, making the approach robust to subject motion during the scan.

Aniket Pramanik, M. Bridget Zimmerman, Mathews Jacob

Computational imaging has been revolutionized by compressed sensing algorithms, which offer guaranteed uniqueness, convergence, and stability properties. Model-based deep learning methods that combine imaging physics with learned regularization priors have emerged as more powerful alternatives for image recovery. The main focus of this paper is to introduce a memory efficient model-based algorithm with similar theoretical guarantees as CS methods. The proposed iterative algorithm alternates between a gradient descent involving the score function and a conjugate gradient algorithm to encourage data consistency. The score function is modeled as a monotone convolutional neural network. Our analysis shows that the monotone constraint is necessary and sufficient to enforce the uniqueness of the fixed point in arbitrary inverse problems. In addition, it also guarantees the convergence to a fixed point, which is robust to input perturbations. We introduce two implementations of the proposed MOL framework, which differ in the way the monotone property is imposed. The first approach enforces a strict monotone constraint, while the second one relies on an approximation. The guarantees are not valid for the second approach in the strict sense. However, our empirical studies show that the convergence and robustness of both approaches are comparable, while the less constrained approximate implementation offers better performance. The proposed deep equilibrium formulation is significantly more memory efficient than unrolled methods, which allows us to apply it to 3D or 2D+time problems that current unrolled algorithms cannot handle.

Fahim Ahmed Zaman, Mathews Jacob, Amanda Chang et al.

Diffusion Probabilistic Models (DPMs) suffer from inefficient inference due to their slow sampling and high memory consumption, which limits their applicability to various medical imaging applications. In this work, we propose a novel conditional diffusion modeling framework (LDSeg) for medical image segmentation, utilizing the learned inherent low-dimensional latent shape manifolds of the target objects and the embeddings of the source image with an end-to-end framework. Conditional diffusion in latent space not only ensures accurate image segmentation for multiple interacting objects, but also tackles the fundamental issues of traditional DPM-based segmentation methods: (1) high memory consumption, (2) time-consuming sampling process, and (3) unnatural noise injection in the forward and reverse processes. The end-to-end training strategy enables robust representation learning in the latent space related to segmentation features, ensuring significantly faster sampling from the posterior distribution for segmentation generation in the inference phase. Our experiments demonstrate that LDSeg achieved state-of-the-art segmentation accuracy on three medical image datasets with different imaging modalities. In addition, we showed that our proposed model was significantly more robust to noise compared to traditional deterministic segmentation models. The code is available at https://github.com/FahimZaman/LDSeg.git.

Aniket Pramanik, Sampada Bhave, Saurav Sajib et al.

Purpose: The aim of this work is to introduce a single model-based deep network that can provide high-quality reconstructions from undersampled parallel MRI data acquired with multiple sequences, acquisition settings and field strengths. Methods: A single unrolled architecture, which offers good reconstructions for multiple acquisition settings, is introduced. The proposed scheme adapts the model to each setting by scaling the CNN features and the regularization parameter with appropriate weights. The scaling weights and regularization parameter are derived using a multi-layer perceptron model from conditional vectors, which represents the specific acquisition setting. The perceptron parameters and the CNN weights are jointly trained using data from multiple acquisition settings, including differences in field strengths, acceleration, and contrasts. The conditional network is validated using datasets acquired with different acquisition settings. Results: The comparison of the adaptive framework, which trains a single model using the data from all the settings, shows that it can offer consistently improved performance for each acquisition condition. The comparison of the proposed scheme with networks that are trained independently for each acquisition setting shows that it requires less training data per acquisition setting to offer good performance. Conclusion: The Ada-MoDL framework enables the use of a single model-based unrolled network for multiple acquisition settings. In addition to eliminating the need to train and store multiple networks for different acquisition settings, this approach reduces the training data needed for each acquisition setting.

Aniket Pramanik, Mathews Jacob

Model-based deep learning methods that combine imaging physics with learned regularization priors have been emerging as powerful tools for parallel MRI acceleration. The main focus of this paper is to determine the utility of the monotone operator learning (MOL) framework in the parallel MRI setting. The MOL algorithm alternates between a gradient descent step using a monotone convolutional neural network (CNN) and a conjugate gradient algorithm to encourage data consistency. The benefits of this approach include similar guarantees as compressive sensing algorithms including uniqueness, convergence, and stability, while being significantly more memory efficient than unrolled methods. We validate the proposed scheme by comparing it with different unrolled algorithms in the context of accelerated parallel MRI for static and dynamic settings.

Jyothi Rikabh Chand, Mathews Jacob

We introduce a novel energy formulation for Plug- and-Play (PnP) image recovery. Traditional PnP methods that use a convolutional neural network (CNN) do not have an energy based formulation. The primary focus of this work is to introduce an energy-based PnP formulation, which relies on a CNN that learns the log of the image prior from training data. The score function is evaluated as the gradient of the energy model, which resembles a UNET with shared encoder and decoder weights. The proposed score function is thus constrained to a conservative vector field, which is the key difference with classical PnP models. The energy-based formulation offers algorithms with convergence guarantees, even when the learned score model is not a contraction. The relaxation of the contraction constraint allows the proposed model to learn more complex priors, thus offering improved performance over traditional PnP schemes. Our experiments in magnetic resonance image reconstruction demonstrates the improved performance offered by the proposed energy model over traditional PnP methods.

Jyothi Rikhab Chand, Mathews Jacob

Solving inverse problems in imaging requires models that support efficient inference, uncertainty quantification, and principled probabilistic reasoning. Energy-Based Models (EBMs), with their interpretable energy landscapes and compositional structure, are well-suited for this task but have historically suffered from high computational costs and training instability. To overcome the historical shortcomings of EBMs, we introduce a fast distillation strategy to transfer the strengths of pre-trained diffusion models into multi-scale EBMs. These distilled EBMs enable efficient sampling and preserve the interpretability and compositionality inherent to potential-based frameworks. Leveraging EBM compositionality, we propose Annealed Langevin Posterior Sampling (ALPS) algorithm for Maximum-A-Posteriori (MAP), Minimum Mean Square Error (MMSE), and uncertainty estimates for inverse problems in imaging. Unlike diffusion models that use complex guidance strategies for latent variables, we perform annealing on static posterior distributions that are well-defined and composable. Experiments on image inpainting and MRI reconstruction demonstrate that our method matches or surpasses diffusion-based baselines in both accuracy and efficiency, while also supporting MAP recovery. Overall, our framework offers a scalable and principled solution for inverse problems in imaging, with potential for practical deployment in scientific and clinical settings. ALPS code is available at the GitHub repository \href{https://github.com/JyoChand/ALPS}{ALPS}.

Hemant Kumar Aggarwal, Mathews Jacob

Modern MRI schemes, which rely on compressed sensing or deep learning algorithms to recover MRI data from undersampled multichannel Fourier measurements, are widely used to reduce scan time. The image quality of these approaches is heavily dependent on the sampling pattern. We introduce a continuous strategy to jointly optimize the sampling pattern and network parameters. We use a multichannel forward model, consisting of a non-uniform Fourier transform with continuously defined sampling locations, to realize the data consistency block within a model-based deep learning image reconstruction scheme. This approach facilitates the joint and continuous optimization of the sampling pattern and the CNN parameters to improve image quality. We observe that the joint optimization of the sampling patterns and the reconstruction module significantly improves the performance of most deep learning reconstruction algorithms. The source code of the proposed joint learning framework is available at https://github.com/hkaggarwal/J-MoDL.

Reinhard Heckel, Mathews Jacob, Akshay Chaudhari et al.

Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.

Jyothi Rikhab Chand, Mathews Jacob

End-to-End (E2E) unrolled optimization frameworks show promise for Magnetic Resonance (MR) image recovery, but suffer from high memory usage during training. In addition, these deterministic approaches do not offer opportunities for sampling from the posterior distribution. In this paper, we introduce a memory-efficient approach for E2E learning of the posterior distribution. We represent this distribution as the combination of a data-consistency-induced likelihood term and an energy model for the prior, parameterized by a Convolutional Neural Network (CNN). The CNN weights are learned from training data in an E2E fashion using maximum likelihood optimization. The learned model enables the recovery of images from undersampled measurements using the Maximum A Posteriori (MAP) optimization. In addition, the posterior model can be sampled to derive uncertainty maps about the reconstruction. Experiments on parallel MR image reconstruction show that our approach performs comparable to the memory-intensive E2E unrolled algorithm, performs better than its memory-efficient counterpart, and can provide uncertainty maps. Our framework paves the way towards MR image reconstruction in 3D and higher dimensions

Fahim Ahmed Zaman, Mathews Jacob, Amanda Chang et al.

Diffusion models have shown impressive performance for image generation, often times outperforming other generative models. Since their introduction, researchers have extended the powerful noise-to-image denoising pipeline to discriminative tasks, including image segmentation. In this work we propose a conditional score-based generative modeling framework for medical image segmentation which relies on a parametric surface representation for the segmentation masks. The surface re-parameterization allows the direct application of standard diffusion theory, as opposed to when the mask is represented as a binary mask. Moreover, we adapted an extended variant of the diffusion technique known as the "cold-diffusion" where the diffusion model can be constructed with deterministic perturbations instead of Gaussian noise, which facilitates significantly faster convergence in the reverse diffusion. We evaluated our method on the segmentation of the left ventricle from 65 transthoracic echocardiogram videos (2230 echo image frames) and compared its performance to the most popular and widely used image segmentation models. Our proposed model not only outperformed the compared methods in terms of segmentation accuracy, but also showed potential in estimating segmentation uncertainties for further downstream analyses due to its inherent generative nature.

Joseph Kettelkamp, Ludovica Romanin, Sarv Priya et al.

We introduce an unsupervised motion-compensated image reconstruction algorithm for free-breathing and ungated 3D cardiac magnetic resonance imaging (MRI). We express the image volume corresponding to each specific motion phase as the deformation of a single static image template. The main contribution of the work is the low-rank model for the compact joint representation of the family of diffeomorphisms, parameterized by the motion phases. The diffeomorphism at a specific motion phase is obtained by integrating a parametric velocity field along a path connecting the reference template phase to the motion phase. The velocity field at different phases is represented using a low-rank model. The static template and the low-rank motion model parameters are learned directly from the k-space data in an unsupervised fashion. The more constrained motion model is observed to offer improved recovery compared to current motion-resolved and motion-compensated algorithms for free-breathing 3D cine MRI.

Jyothi Rikhab Chand, Mathews Jacob

Current end-to-end (E2E) and plug-and-play (PnP) image reconstruction algorithms approximate the maximum a posteriori (MAP) estimate but cannot offer sampling from the posterior distribution, like diffusion models. By contrast, it is challenging for diffusion models to be trained in an E2E fashion. This paper introduces a Deep End-to-End Posterior ENergy (DEEPEN) framework, which enables MAP estimation as well as sampling. We learn the parameters of the posterior, which is the sum of the data consistency error and the negative log-prior distribution, using maximum likelihood optimization in an E2E fashion. The proposed approach does not require algorithm unrolling, and hence has a smaller computational and memory footprint than current E2E methods, while it does not require contraction constraints typically needed by current PnP methods. Our results demonstrate that DEEPEN offers improved performance than current E2E and PnP models in the MAP setting, while it also offers faster sampling compared to diffusion models. In addition, the learned energy-based model is observed to be more robust to changes in image acquisition settings.

Jyothi Rikhab Chand, Mathews Jacob

We propose a multi-scale deep energy model that is strongly convex in the local neighbourhood around the data manifold to represent its probability density, with application in inverse problems. In particular, we represent the negative log-prior as a multi-scale energy model parameterized by a Convolutional Neural Network (CNN). We restrict the gradient of the CNN to be locally monotone, which constrains the model as a Locally Convex Multi-Scale Energy (LC-MuSE). We use the learned energy model in image-based inverse problems, where the formulation offers several desirable properties: i) uniqueness of the solution, ii) convergence guarantees to a minimum of the inverse problem, and iii) robustness to input perturbations. In the context of parallel Magnetic Resonance (MR) image reconstruction, we show that the proposed method performs better than the state-of-the-art convex regularizers, while the performance is comparable to plug-and-play regularizers and end-to-end trained methods.

Reza Ghorbani, Jyothi Rikhab Chand, Chu-Yu Lee et al.

Three-dimensional (3D) multi-slab acquisition is a technique frequently employed in high-resolution diffusion-weighted MRI in order to achieve the best signal-to-noise ratio (SNR) efficiency. However, this technique is limited by slab boundary artifacts that cause intensity fluctuations and aliasing between slabs which reduces the accuracy of anatomical imaging. Addressing this issue is crucial for advancing diffusion MRI quality and making high-resolution imaging more feasible for clinical and research applications. In this work, we propose a regularized slab profile encoding (PEN) method within a Plug-and-Play ADMM framework, incorporating multi-scale energy (MuSE) regularization to effectively improve the slab combined reconstruction. Experimental results demonstrate that the proposed method significantly improves image quality compared to non-regularized and TV-regularized PEN approaches. The regularized PEN framework provides a more robust and efficient solution for high-resolution 3D diffusion MRI, potentially enabling clearer, more reliable anatomical imaging across various applications.

Qing Zou, Luis A. Torres, Sean B. Fain et al.

We introduce an unsupervised motion-compensated reconstruction scheme for high-resolution free-breathing pulmonary MRI. We model the image frames in the time series as the deformed version of the 3D template image volume. We assume the deformation maps to be points on a smooth manifold in high-dimensional space. Specifically, we model the deformation map at each time instant as the output of a CNN-based generator that has the same weight for all time-frames, driven by a low-dimensional latent vector. The time series of latent vectors account for the dynamics in the dataset, including respiratory motion and bulk motion. The template image volume, the parameters of the generator, and the latent vectors are learned directly from the k-t space data in an unsupervised fashion. Our experimental results show improved reconstructions compared to state-of-the-art methods, especially in the context of bulk motion during the scans.

Aniket Pramanik, Mathews Jacob

Model-based deep learning (MoDL) algorithms that rely on unrolling are emerging as powerful tools for image recovery. In this work, we introduce a novel monotone operator learning framework to overcome some of the challenges associated with current unrolled frameworks, including high memory cost, lack of guarantees on robustness to perturbations, and low interpretability. Unlike current unrolled architectures that use finite number of iterations, we use the deep equilibrium (DEQ) framework to iterate the algorithm to convergence and to evaluate the gradient of the convolutional neural network blocks using Jacobian iterations. This approach significantly reduces the memory demand, facilitating the extension of MoDL algorithms to high dimensional problems. We constrain the CNN to be a monotone operator, which allows us to introduce algorithms with guaranteed convergence properties and robustness guarantees. We demonstrate the utility of the proposed scheme in the context of parallel MRI.

Maneesh John, Hemant Kumar Aggarwal, Qing Zou et al.

Deep learning algorithms that rely on extensive training data are revolutionizing image recovery from ill-posed measurements. Training data is scarce in many imaging applications, including ultra-high-resolution imaging. The deep image prior (DIP) algorithm was introduced for single-shot image recovery, completely eliminating the need for training data. A challenge with this scheme is the need for early stopping to minimize the overfitting of the CNN parameters to the noise in the measurements. We introduce a generalized Stein's unbiased risk estimate (GSURE) loss metric to minimize the overfitting. Our experiments show that the SURE-DIP approach minimizes the overfitting issues, thus offering significantly improved performance over classical DIP schemes. We also use the SURE-DIP approach with model-based unrolling architectures, which offers improved performance over direct inversion schemes.

Qing Zou, Abdul Haseeb Ahmed, Prashant Nagpal et al.

Free-breathing cardiac MRI schemes are emerging as competitive alternatives to breath-held cine MRI protocols, enabling applicability to pediatric and other population groups that cannot hold their breath. Because the data from the slices are acquired sequentially, the cardiac/respiratory motion patterns may be different for each slice; current free-breathing approaches perform independent recovery of each slice. In addition to not being able to exploit the inter-slice redundancies, manual intervention or sophisticated post-processing methods are needed to align the images post-recovery for quantification. To overcome these challenges, we propose an unsupervised variational deep manifold learning scheme for the joint alignment and reconstruction of multislice dynamic MRI. The proposed scheme jointly learns the parameters of the deep network as well as the latent vectors for each slice, which capture the motion-induced dynamic variations, from the k-t space data of the specific subject. The variational framework minimizes the non-uniqueness in the representation, thus offering improved alignment and reconstructions.

Qing Zou, Luis A. Torres, Sean B. Fain et al.

We introduce an unsupervised deep manifold learning algorithm for motion-compensated dynamic MRI. We assume that the motion fields in a free-breathing lung MRI dataset live on a manifold. The motion field at each time instant is modeled as the output of a deep generative model, driven by low-dimensional time-varying latent vectors that capture the temporal variability. The images at each time instant are modeled as the deformed version of an image template using the above motion fields. The template, the parameters of the deep generator, and the latent vectors are learned from the k-t space data in an unsupervised fashion. The manifold motion model serves as a regularizer, making the joint estimation of the motion fields and images from few radial spokes/frame well-posed. The utility of the algorithm is demonstrated in the context of motion-compensated high-resolution lung MRI.

Aniket Pramanik, Xiaodong Wu, Mathews Jacob

The volume estimation of brain regions from MRI data is a key problem in many clinical applications, where the acquisition of data at high spatial resolution is desirable. While parallel MRI and constrained image reconstruction algorithms can accelerate the scans, image reconstruction artifacts are inevitable, especially at high acceleration factors. We introduce a novel image domain deep-learning framework for calibrationless parallel MRI reconstruction, coupled with a segmentation network to improve image quality and to reduce the vulnerability of current segmentation algorithms to image artifacts resulting from acceleration. The combination of the proposed image domain deep calibrationless approach with the segmentation algorithm offers improved image quality, while increasing the accuracy of the segmentations. The novel architecture with an encoder shared between the reconstruction and segmentation tasks is seen to reduce the need for segmented training datasets. In particular, the proposed few-shot training strategy requires only 10% of segmented datasets to offer good performance.

Aniket Pramanik, Mathews Jacob

The main focus of this work is a novel framework for the joint reconstruction and segmentation of parallel MRI (PMRI) brain data. We introduce an image domain deep network for calibrationless recovery of undersampled PMRI data. The proposed approach is the deep-learning (DL) based generalization of local low-rank based approaches for uncalibrated PMRI recovery including CLEAR [6]. Since the image domain approach exploits additional annihilation relations compared to k-space based approaches, we expect it to offer improved performance. To minimize segmentation errors resulting from undersampling artifacts, we combined the proposed scheme with a segmentation network and trained it in an end-to-end fashion. In addition to reducing segmentation errors, this approach also offers improved reconstruction performance by reducing overfitting; the reconstructed images exhibit reduced blurring and sharper edges than independently trained reconstruction network.

Hemant Kumar Aggarwal, Mathews Jacob

Deep learning image reconstruction algorithms often suffer from model mismatches when the acquisition scheme differs significantly from the forward model used during training. We introduce a Generalized Stein's Unbiased Risk Estimate (GSURE) loss metric to adapt the network to the measured k-space data and minimize model misfit impact. Unlike current methods that rely on the mean square error in kspace, the proposed metric accounts for noise in the measurements. This makes the approach less vulnerable to overfitting, thus offering improved reconstruction quality compared to schemes that rely on mean-square error. This approach may be useful to rapidly adapt pre-trained models to new acquisition settings (e.g., multi-site) and different contrasts than training data

Hemant Kumar Aggarwal, Aniket Pramanik, Maneesh John et al.

Image reconstruction using deep learning algorithms offers improved reconstruction quality and lower reconstruction time than classical compressed sensing and model-based algorithms. Unfortunately, clean and fully sampled ground-truth data to train the deep networks is often unavailable in several applications, restricting the applicability of the above methods. We introduce a novel metric termed the ENsemble Stein's Unbiased Risk Estimate (ENSURE) framework, which can be used to train deep image reconstruction algorithms without fully sampled and noise-free images. The proposed framework is the generalization of the classical SURE and GSURE formulation to the setting where the images are sampled by different measurement operators, chosen randomly from a set. We evaluate the expectation of the GSURE loss functions over the sampling patterns to obtain the ENSURE loss function. We show that this loss is an unbiased estimate for the true mean-square error, which offers a better alternative to GSURE, which only offers an unbiased estimate for the projected error. Our experiments show that the networks trained with this loss function can offer reconstructions comparable to the supervised setting. While we demonstrate this framework in the context of MR image recovery, the ENSURE framework is generally applicable to arbitrary inverse problems.

Aniket Pramanik, Hemant Aggarwal, Mathews Jacob

Structured low-rank (SLR) algorithms, which exploit annihilation relations between the Fourier samples of a signal resulting from different properties, is a powerful image reconstruction framework in several applications. This scheme relies on low-rank matrix completion to estimate the annihilation relations from the measurements. The main challenge with this strategy is the high computational complexity of matrix completion. We introduce a deep learning (DL) approach to significantly reduce the computational complexity. Specifically, we use a convolutional neural network (CNN)-based filterbank that is trained to estimate the annihilation relations from imperfect (under-sampled and noisy) k-space measurements of Magnetic Resonance Imaging (MRI). The main reason for the computational efficiency is the pre-learning of the parameters of the non-linear CNN from exemplar data, compared to SLR schemes that learn the linear filterbank parameters from the dataset itself. Experimental comparisons show that the proposed scheme can enable calibration-less parallel MRI; it can offer performance similar to SLR schemes while reducing the runtime by around three orders of magnitude. Unlike pre-calibrated and self-calibrated approaches, the proposed uncalibrated approach is insensitive to motion errors and affords higher acceleration. The proposed scheme also incorporates image domain priors that are complementary, thus significantly improving the performance over that of SLR schemes.

Aniket Pramanik, Hemant Aggarwal, Mathews Jacob

We introduce a fast model based deep learning approach for calibrationless parallel MRI reconstruction. The proposed scheme is a non-linear generalization of structured low rank (SLR) methods that self learn linear annihilation filters from the same subject. It pre-learns non-linear annihilation relations in the Fourier domain from exemplar data. The pre-learning strategy significantly reduces the computational complexity, making the proposed scheme three orders of magnitude faster than SLR schemes. The proposed framework also allows the use of a complementary spatial domain prior; the hybrid regularization scheme offers improved performance over calibrated image domain MoDL approach. The calibrationless strategy minimizes potential mismatches between calibration data and the main scan, while eliminating the need for a fully sampled calibration region.

Mathews Jacob, Merry P. Mani, Jong Chul Ye

In this survey, we provide a detailed review of recent advances in the recovery of continuous domain multidimensional signals from their few non-uniform (multichannel) measurements using structured low-rank matrix completion formulation. This framework is centered on the fundamental duality between the compactness (e.g., sparsity) of the continuous signal and the rank of a structured matrix, whose entries are functions of the signal. This property enables the reformulation of the signal recovery as a low-rank structured matrix completion, which comes with performance guarantees. We will also review fast algorithms that are comparable in complexity to current compressed sensing methods, which enables the application of the framework to large-scale magnetic resonance (MR) recovery problems. The remarkable flexibility of the formulation can be used to exploit signal properties that are difficult to capture by current sparse and low-rank optimization strategies. We demonstrate the utility of the framework in a wide range of MR imaging (MRI) applications, including highly accelerated imaging, calibration-free acquisition, MR artifact correction, and ungated dynamic MRI.

Aniket Pramanik, Hemant Kumar Aggarwal, Mathews Jacob

We introduce a model based off-the-grid image reconstruction algorithm using deep learned priors. The main difference of the proposed scheme with current deep learning strategies is the learning of non-linear annihilation relations in Fourier space. We rely on a model based framework, which allows us to use a significantly smaller deep network, compared to direct approaches that also learn how to invert the forward model. Preliminary comparisons against image domain MoDL approach demonstrates the potential of the off-the-grid formulation. The main benefit of the proposed scheme compared to structured low-rank methods is the quite significant reduction in computational complexity.

Hemant Kumar Aggarwal, Merry P. Mani, Mathews Jacob

We introduce a model-based deep learning architecture termed MoDL-MUSSELS for the correction of phase errors in multishot diffusion-weighted echo-planar MRI images. The proposed algorithm is a generalization of existing MUSSELS algorithm with similar performance but with significantly reduced computational complexity. In this work, we show that an iterative re-weighted least-squares implementation of MUSSELS alternates between a multichannel filter bank and the enforcement of data consistency. The multichannel filter bank projects the data to the signal subspace thus exploiting the phase relations between shots. Due to the high computational complexity of self-learned filter bank, we propose to replace it with a convolutional neural network (CNN) whose parameters are learned from exemplary data. The proposed CNN is a hybrid model involving a multichannel CNN in the k-space and another CNN in the image space. The k-space CNN exploits the phase relations between the shot images, while the image domain network is used to project the data to an image manifold. The experiments show that the proposed scheme can yield reconstructions that are comparable to state of the art methods while offering several orders of magnitude reduction in run-time.

Sampurna Biswas, Hemant K. Aggarwal, Sunrita Poddar et al.

We introduce a model-based reconstruction framework with deep learned (DL) and smoothness regularization on manifolds (STORM) priors to recover free breathing and ungated (FBU) cardiac MRI from highly undersampled measurements. The DL priors enable us to exploit the local correlations, while the STORM prior enables us to make use of the extensive non-local similarities that are subject dependent. We introduce a novel model-based formulation that allows the seamless integration of deep learning methods with available prior information, which current deep learning algorithms are not capable of. The experimental results demonstrate the preliminary potential of this work in accelerating FBU cardiac MRI.

Arvind Balachandrasekaran, Merry Mani, Mathews Jacob

We introduce a structured low rank algorithm for the calibration-free compensation of field inhomogeneity artifacts in Echo Planar Imaging (EPI) MRI data. We acquire the data using two EPI readouts that differ in echo-time (TE). Using time segmentation, we reformulate the field inhomogeneity compensation problem as the recovery of an image time series from highly undersampled Fourier measurements. The temporal profile at each pixel is modeled as a single exponential, which is exploited to fill in the missing entries. We show that the exponential behavior at each pixel, along with the spatial smoothness of the exponential parameters, can be exploited to derive a 3D annihilation relation in the Fourier domain. This relation translates to a low rank property on a structured multi-fold Toeplitz matrix, whose entries correspond to the measured k-space samples. We introduce a fast two-step algorithm for the completion of the Toeplitz matrix from the available samples. In the first step, we estimate the null space vectors of the Toeplitz matrix using only its fully sampled rows. The null space is then used to estimate the signal subspace, which facilitates the efficient recovery of the time series of images. We finally demonstrate the proposed approach on spherical MR phantom data and human data and show that the artifacts are significantly reduced. The proposed approach could potentially be used to compensate for time varying field map variations in dynamic applications such as functional MRI.

Sunrita Poddar, Yasir Mohsin, Deidra Ansah et al.

We introduce a novel bandlimited manifold framework and an algorithm to recover freebreathing and ungated cardiac MR images from highly undersampled measurements. The image frames in the free breathing and ungated dataset are assumed to be points on a bandlimited manifold. We introduce a novel kernel low-rank algorithm to estimate the manifold structure (Laplacian) from a navigator-based acquisition scheme. The structure of the manifold is then used to recover the images from highly undersampled measurements. A computationally efficient algorithm, which relies on the bandlimited approximation of the Laplacian matrix, is used to recover the images. The proposed scheme is demonstrated on several patients with different breathing patterns and cardiac rates, without requiring the need for manually tuning the reconstruction parameters in each case. The proposed scheme enabled the recovery of free-breathing and ungated data, providing reconstructions that are qualitatively similar to breath-held scans performed on the same patients. This shows the potential of the technique as a clinical protocol for free-breathing cardiac scans.

Sunrita Poddar, Mathews Jacob

The analysis of large datasets is often complicated by the presence of missing entries, mainly because most of the current machine learning algorithms are designed to work with full data. The main focus of this work is to introduce a clustering algorithm, that will provide good clustering even in the presence of missing data. The proposed technique solves an $\ell_0$ fusion penalty based optimization problem to recover the clusters. We theoretically analyze the conditions needed for the successful recovery of the clusters. We also propose an algorithm to solve a relaxation of this problem using saturating non-convex fusion penalties. The method is demonstrated on simulated and real datasets, and is observed to perform well in the presence of large fractions of missing entries.

Sunrita Poddar, Mathews Jacob

We introduce a continuous domain framework for the recovery of points on a surface in high dimensional space, represented as the zero-level set of a bandlimited function. We show that the exponential maps of the points on the surface satisfy annihilation relations, implying that they lie in a finite dimensional subspace. The subspace properties are used to derive sampling conditions, which will guarantee the perfect recovery of the surface from finite number of points. We rely on nuclear norm minimization to exploit the low-rank structure of the maps to recover the points from noisy measurements. Since the direct estimation of the surface is computationally prohibitive in very high dimensions, we propose an iterative reweighted algorithm using the "kernel trick". The iterative algorithm reveals deep links to Laplacian based algorithms widely used in graph signal processing; the theory and the sampling conditions can serve as a basis for discrete-continuous domain processing of signals on a graph.

Sunrita Poddar, Mathews Jacob

We introduce a framework for the recovery of points on a smooth surface in high-dimensional space, with application to dynamic imaging. We assume the surface to be the zero-level set of a bandlimited function. We show that the exponential maps of the points on the surface satisfy annihilation relations, implying that they lie in a finite dimensional subspace. We rely on nuclear norm minimization of the maps to recover the points from noisy and undersampled measurements. Since this direct approach suffers from the curse of dimensionality, we introduce an iterative reweighted algorithm that uses the "kernel trick". The resulting algorithm has similarities to iterative algorithms used in graph signal processing (GSP); this framework can be seen as a continuous domain alternative to discrete GSP theory. The use of the algorithm in recovering free breathing and ungated cardiac data shows the potential of this framework in practical applications.

Hemant Kumar Aggarwal, Merry P. Mani, Mathews Jacob

We introduce a model-based image reconstruction framework with a convolution neural network (CNN) based regularization prior. The proposed formulation provides a systematic approach for deriving deep architectures for inverse problems with the arbitrary structure. Since the forward model is explicitly accounted for, a smaller network with fewer parameters is sufficient to capture the image information compared to black-box deep learning approaches, thus reducing the demand for training data and training time. Since we rely on end-to-end training, the CNN weights are customized to the forward model, thus offering improved performance over approaches that rely on pre-trained denoisers. The main difference of the framework from existing end-to-end training strategies is the sharing of the network weights across iterations and channels. Our experiments show that the decoupling of the number of iterations from the network complexity offered by this approach provides benefits including lower demand for training data, reduced risk of overfitting, and implementations with significantly reduced memory footprint. We propose to enforce data-consistency by using numerical optimization blocks such as conjugate gradients algorithm within the network; this approach offers faster convergence per iteration, compared to methods that rely on proximal gradients steps to enforce data consistency. Our experiments show that the faster convergence translates to improved performance, especially when the available GPU memory restricts the number of iterations.

Weiyu Xu, Jirong Yi, Soura Dasgupta et al.

We consider the problem of recovering the superposition of $R$ distinct complex exponential functions from compressed non-uniform time-domain samples. Total Variation (TV) minimization or atomic norm minimization was proposed in the literature to recover the $R$ frequencies or the missing data. However, it is known that in order for TV minimization and atomic norm minimization to recover the missing data or the frequencies, the underlying $R$ frequencies are required to be well-separated, even when the measurements are noiseless. This paper shows that the Hankel matrix recovery approach can super-resolve the $R$ complex exponentials and their frequencies from compressed non-uniform measurements, regardless of how close their frequencies are to each other. We propose a new concept of orthonormal atomic norm minimization (OANM), and demonstrate that the success of Hankel matrix recovery in separation-free super-resolution comes from the fact that the nuclear norm of a Hankel matrix is an orthonormal atomic norm. More specifically, we show that, in traditional atomic norm minimization, the underlying parameter values $\textbf{must}$ be well separated to achieve successful signal recovery, if the atoms are changing continuously with respect to the continuously-valued parameter. In contrast, for the OANM, it is possible the OANM is successful even though the original atoms can be arbitrarily close. As a byproduct of this research, we provide one matrix-theoretic inequality of nuclear norm, and give its proof from the theory of compressed sensing.

Sunrita Poddar, Mathews Jacob

The presence of missing entries in data often creates challenges for pattern recognition algorithms. Traditional algorithms for clustering data assume that all the feature values are known for every data point. We propose a method to cluster data in the presence of missing information. Unlike conventional clustering techniques where every feature is known for each point, our algorithm can handle cases where a few feature values are unknown for every point. For this more challenging problem, we provide theoretical guarantees for clustering using a $\ell_0$ fusion penalty based optimization problem. Furthermore, we propose an algorithm to solve a relaxation of this problem using saturating non-convex fusion penalties. It is observed that this algorithm produces solutions that degrade gradually with an increase in the fraction of missing feature values. We demonstrate the utility of the proposed method using a simulated dataset, the Wine dataset and also an under-sampled cardiac MRI dataset. It is shown that the proposed method is a promising clustering technique for datasets with large fractions of missing entries.

Arvind Balachandrasekaran, Vincent Magnotta, Mathews Jacob

We introduce a structured low rank matrix completion algorithm to recover a series of images from their under-sampled measurements, where the signal along the parameter dimension at every pixel is described by a linear combination of exponentials. We exploit the exponential behavior of the signal at every pixel, along with the spatial smoothness of the exponential parameters to derive an annihilation relation in the Fourier domain. This relation translates to a low-rank property on a structured matrix constructed from the Fourier samples. We enforce the low rank property of the structured matrix as a regularization prior to recover the images. Since the direct use of current low rank matrix recovery schemes to this problem is associated with high computational complexity and memory demand, we adopt an iterative re-weighted least squares (IRLS) algorithm, which facilitates the exploitation of the convolutional structure of the matrix. Novel approximations involving two dimensional Fast Fourier Transforms (FFT) are introduced to drastically reduce the memory demand and computational complexity, which facilitates the extension of structured low rank methods to large scale three dimensional problems. We demonstrate our algorithm in the MR parameter mapping setting and show improvement over the state-of-the-art methods.

Greg Ongie, Mathews Jacob

Fourier domain structured low-rank matrix priors are emerging as powerful alternatives to traditional image recovery methods such as total variation and wavelet regularization. These priors specify that a convolutional structured matrix, i.e., Toeplitz, Hankel, or their multi-level generalizations, built from Fourier data of the image should be low-rank. The main challenge in applying these schemes to large-scale problems is the computational complexity and memory demand resulting from lifting the image data to a large scale matrix. We introduce a fast and memory efficient approach called the Generic Iterative Reweighted Annihilation Filter (GIRAF) algorithm that exploits the convolutional structure of the lifted matrix to work in the original un-lifted domain, thus considerably reducing the complexity. Our experiments on the recovery of images from undersampled Fourier measurements show that the resulting algorithm is considerably faster than previously proposed algorithms, and can accommodate much larger problem sizes than previously studied.

Arvind Balachandrasekaran, Mathews Jacob

We propose a structured low rank matrix completion algorithm to recover a time series of images consisting of linear combination of exponential parameters at every pixel, from under-sampled Fourier measurements. The spatial smoothness of these parameters is exploited along with the exponential structure of the time series at every pixel, to derive an annihilation relation in the $k-t$ domain. This annihilation relation translates into a structured low rank matrix formed from the $k-t$ samples. We demonstrate the algorithm in the parameter mapping setting and show significant improvement over state of the art methods.

Greg Ongie, Mathews Jacob

We introduce a method to recover a continuous domain representation of a piecewise constant two-dimensional image from few low-pass Fourier samples. Assuming the edge set of the image is localized to the zero set of a trigonometric polynomial, we show the Fourier coefficients of the partial derivatives of the image satisfy a linear annihilation relation. We present necessary and sufficient conditions for unique recovery of the image from finite low-pass Fourier samples using the annihilation relation. We also propose a practical two-stage recovery algorithm which is robust to model-mismatch and noise. In the first stage we estimate a continuous domain representation of the edge set of the image. In the second stage we perform an extrapolation in Fourier domain by a least squares two-dimensional linear prediction, which recovers the exact Fourier coefficients of the underlying image. We demonstrate our algorithm on the super-resolution recovery of MRI phantoms and real MRI data from low-pass Fourier samples, which shows benefits over standard approaches for single-image super-resolution MRI.

Greg Ongie, Mathews Jacob

We introduce a Prony-like method to recover a continuous domain 2-D piecewise smooth image from few of its Fourier samples. Assuming the discontinuity set of the image is localized to the zero level-set of a trigonometric polynomial, we show the Fourier transform coefficients of partial derivatives of the signal satisfy an annihilation relation. We present necessary and sufficient conditions for unique recovery of piecewise constant images using the above annihilation relation. We pose the recovery of the Fourier coefficients of the signal from the measurements as a convex matrix completion algorithm, which relies on the lifting of the Fourier data to a structured low-rank matrix; this approach jointly estimates the signal and the annihilating filter. Finally, we demonstrate our algorithm on the recovery of MRI phantoms from few low-resolution Fourier samples.

Greg Ongie, Mathews Jacob

We propose a two-stage algorithm for the super-resolution of MR images from their low-frequency k-space samples. In the first stage we estimate a resolution-independent mask whose zeros represent the edges of the image. This builds off recent work extending the theory of sampling signals of finite rate of innovation (FRI) to two-dimensional curves. We enable its application to MRI by proposing extensions of the signal models allowed by FRI theory, and by developing a more robust and efficient means to determine the edge mask. In the second stage of the scheme, we recover the super-resolved MR image using the discretized edge mask as an image prior. We evaluate our scheme on simulated single-coil MR data obtained from analytical phantoms, and compare against total variation reconstructions. Our experiments show improved performance in both noiseless and noisy settings.

Sampurna Biswas, Sunrita Poddar, Soura Dasgupta et al.

We consider the recovery of a low rank and jointly sparse matrix from under sampled measurements of its columns. This problem is highly relevant in the recovery of dynamic MRI data with high spatio-temporal resolution, where each column of the matrix corresponds to a frame in the image time series; the matrix is highly low-rank since the frames are highly correlated. Similarly the non-zero locations of the matrix in appropriate transform/frame domains (e.g. wavelet, gradient) are roughly the same in different frame. The superset of the support can be safely assumed to be jointly sparse. Unlike the classical multiple measurement vector (MMV) setup that measures all the snapshots using the same matrix, we consider each snapshot to be measured using a different measurement matrix. We show that this approach reduces the total number of measurements, especially when the rank of the matrix is much smaller than than its sparsity. Our experiments in the context of dynamic imaging shows that this approach is very useful in realizing free breathing cardiac MRI.

Sampurna Biswas, Sunrita Poddar, Soura Dasgupta et al.

We introduce a two step algorithm with theoretical guarantees to recover a jointly sparse and low-rank matrix from undersampled measurements of its columns. The algorithm first estimates the row subspace of the matrix using a set of common measurements of the columns. In the second step, the subspace aware recovery of the matrix is solved using a simple least square algorithm. The results are verified in the context of recovering CINE data from undersampled measurements; we obtain good recovery when the sampling conditions are satisfied.

Sajan Goud Lingala, Edward DiBella, Mathews Jacob

We propose a novel deformation corrected compressed sensing (DC-CS) framework to recover dynamic magnetic resonance images from undersampled measurements. We introduce a generalized formulation that is capable of handling a wide class of sparsity/compactness priors on the deformation corrected dynamic signal. In this work, we consider example compactness priors such as sparsity in temporal Fourier domain, sparsity in temporal finite difference domain, and nuclear norm penalty to exploit low rank structure. Using variable splitting, we decouple the complex optimization problem to simpler and well understood sub problems; the resulting algorithm alternates between simple steps of shrinkage based denoising, deformable registration, and a quadratic optimization step. Additionally, we employ efficient continuation strategies to minimize the risk of convergence to local minima. The proposed formulation contrasts with existing DC-CS schemes that are customized for free breathing cardiac cine applications, and other schemes that rely on fully sampled reference frames or navigator signals to estimate the deformation parameters. The efficient decoupling enabled by the proposed scheme allows its application to a wide range of applications including contrast enhanced dynamic MRI. Through experiments on numerical phantom and in vivo myocardial perfusion MRI datasets, we demonstrate the utility of the proposed DC-CS scheme in providing robust reconstructions with reduced motion artifacts over classical compressed sensing schemes that utilize the compact priors on the original deformation un-corrected signal.

Yasir Q. Moshin, Greg Ongie, Mathews Jacob

We introduce a fast iterative non-local shrinkage algorithm to recover MRI data from undersampled Fourier measurements. This approach is enabled by the reformulation of current non-local schemes as an alternating algorithm to minimize a global criterion. The proposed algorithm alternates between a non-local shrinkage step and a quadratic subproblem. We derive analytical shrinkage rules for several penalties that are relevant in non-local regularization. The redundancy in the searches used to evaluate the shrinkage steps are exploited using filtering operations. The resulting algorithm is observed to be considerably faster than current alternating non-local algorithms. The comparisons of the proposed scheme with state-of-the-art regularization schemes show a considerable reduction in alias artifacts and preservation of edges.