arXiv subjects

Andreas Kofler

Publications and source records attributed to Andreas Kofler.

At least 19 recordsLinked to original sources

arXiv2026

DREAM: Deep-Reparametrization of Adaptive Regularization Maps for Fast Zero-Shot Self-Supervised Learning

Adaptive regularization is an effective means of improving the flexibility of classical variational reconstruction methods while retaining their interpretability and mathematical structure. In this work, we propose an approach for learning deep-reparameterized adaptive regularization maps (DREAM) for Total Variation (TV) and Total Generalized Variation (TGV) through algorithm unrolling in a zero-shot, self-supervised setting, requiring no access to large paired datasets. We first validate DREAM on a two-dimensional image-denoising problem and then apply it to large-scale dynamic MRI reconstruction. The resulting adaptive models are theoretically grounded, as they retain the convergence properties of the primal-dual algorithm used as the building block of the unrolled architecture. Our results show that the regularization parameter maps can be learned efficiently, requiring substantially fewer weight updates than state-of-the-art methods to achieve comparable performance. We further demonstrate that the CNN parametrization of the maps acts as an implicit prior and provides effective dimensionality reduction, outperforming direct optimization of the adaptive parameters. Across both applications, the performance gap between supervised and zero-shot training is smaller for DREAM than for the end-to-end deep-learning methods considered for comparison. Remarkably, in dynamic cardiac MRI reconstruction, zero-shot training matches the performance of the supervised model. Moreover, the learned adaptive maps are highly interpretable, providing a compelling alternative to purely deep-learning-based methods when reference data are difficult to obtain.

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arXiv2026

Learning spatially varying regularisation parameters of low regularity for image reconstruction

In this chapter, we review and discuss the regularity properties of spatially adaptive regularisation weight functions used in variational image reconstruction. Incorporating such weights into classical model-based regularisers, such as Total Variation (TV) and Total Generalised Variation (TGV), allows the regularisation strength to vary across the image and adapt to local image content. When appropriately estimated, these weights can thus significantly improve edge and detail preservation in the reconstructions. We review the existing theoretical literature on this topic for different regularity classes, including constant, continuous, and piecewise constant functions. Our discussion is motivated by recent work on hybrid image reconstruction methods that combine model-based regularisation with deep neural networks to learn highly adaptive regularisation weights. In particular, we discuss how the structural properties of these weights influence the reconstruction from both theoretical and practical perspectives. Through representative examples in image denoising and magnetic resonance imaging (MRI) reconstruction, we demonstrate that the learned weights are often of low regularity and can adapt not only to the image structure but also to the specific noise realisation. We conclude by highlighting several directions for future research on this topic.

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arXiv2026

Learning spatially adaptive sparsity level maps for arbitrary convolutional dictionaries

State-of-the-art learned reconstruction methods often rely on black-box modules that, despite their strong performance, raise questions about their interpretability and robustness. Here, we build on a recently proposed image reconstruction method, which is based on embedding data-driven information into a model-based convolutional dictionary regularization via neural network-inferred spatially adaptive sparsity level maps. By means of improved network design and dedicated training strategies, we extend the method to achieve filter-permutation invariance as well as the possibility to change the convolutional dictionary at inference time. We apply our method to low-field MRI and compare it to several other recent deep learning-based methods, also on in vivo data, where the benefit of using a different dictionary is demonstrated. We further assess the method's robustness when tested on in- and out-of-distribution data. When tested on the latter, the proposed method suffers less from the data distribution shift compared to the other learned methods, which we attribute to its reduced reliance on training data due to its underlying model-based reconstruction component.

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arXiv2025

MRpro: open framework for model-based, learned, and quantitative MR imaging

We preseent an open-source image reconstruction package built upon PyTorch, enabling modern deep-learning reconstructions. It uses open data formats for input and output (ISMRMRD, DICOM, NIfTI), allowing easy integration into existing pipelines and support for data from different devices. The framework comprises three main areas. First, it provides unified data structures for the consistent manipulation of MR datasets and their associated metadata (e.g., k-space trajectories). Second, it offers a library of composable operators, proximable functionals, and optimization algorithms, including a unified Fourier operator for all common trajectories and operators specifically developed for low-field applications, such as a B0-correction operator. These components are used to create ready-to-use implementations of key reconstruction algorithms. Third, for deep learning, MRpro includes essential building blocks such as data-consistency layers, differentiable optimization layers, state-of-the-art backbone networks, and access to public datasets to facilitate reproducibility. We demonstrate MRpro across automatic reconstruction, iterative SENSE, deep-learning-based reconstruction, and quantitative parameter estimation. Applications use public and simulated datasets and measured lowfield data acquired at 0.3 T, 0.6 T, and 47 mT.

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arXiv2025

Learning Spatially Adaptive $\ell_1$-Norms Weights for Convolutional Synthesis Regularization

We propose an unrolled algorithm approach for learning spatially adaptive parameter maps in the framework of convolutional synthesis-based $\ell_1$ regularization. More precisely, we consider a family of pre-trained convolutional filters and estimate deeply parametrized spatially varying parameters applied to the sparse feature maps by means of unrolling a FISTA algorithm to solve the underlying sparse estimation problem. The proposed approach is evaluated for image reconstruction of low-field MRI and compared to spatially adaptive and non-adaptive analysis-type procedures relying on Total Variation regularization and to a well-established model-based deep learning approach. We show that the proposed approach produces visually and quantitatively comparable results with the latter approaches and at the same time remains highly interpretable. In particular, the inferred parameter maps quantify the local contribution of each filter in the reconstruction, which provides valuable insight into the algorithm mechanism and could potentially be used to discard unsuited filters.

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arXiv2025

Deep unrolling for learning optimal spatially varying regularisation parameters for Total Generalised Variation

We extend a recently introduced deep unrolling framework for learning spatially varying regularisation parameters in inverse imaging problems to the case of Total Generalised Variation (TGV). The framework combines a deep convolutional neural network (CNN) inferring the two spatially varying TGV parameters with an unrolled algorithmic scheme that solves the corresponding variational problem. The two subnetworks are jointly trained end-to-end in a supervised fashion and as such the CNN learns to compute those parameters that drive the reconstructed images as close to the ground truth as possible. Numerical results in image denoising and MRI reconstruction show a significant qualitative and quantitative improvement compared to the best TGV scalar parameter case as well as to other approaches employing spatially varying parameters computed by unsupervised methods. We also observe that the inferred spatially varying parameter maps have a consistent structure near the image edges, asking for further theoretical investigations. In particular, the parameter that weighs the first-order TGV term has a triple-edge structure with alternating high-low-high values whereas the one that weighs the second-order term attains small values in a large neighbourhood around the edges.

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arXiv2025

MR imaging in the low-field: Leveraging the power of machine learning

Recent innovations in Magnetic Resonance Imaging (MRI) hardware and software have reignited interest in low-field ($<1\,\mathrm{T}$) and ultra-low-field MRI ($<0.1\,\mathrm{T}$). These technologies offer advantages such as lower power consumption, reduced specific absorption rate, reduced field-inhomogeneities, and cost-effectiveness, presenting a promising alternative for resource-limited and point-of-care settings. However, low-field MRI faces inherent challenges like reduced signal-to-noise ratio and therefore, potentially lower spatial resolution or longer scan times. This chapter examines the challenges and opportunities of low-field and ultra-low-field MRI, with a focus on the role of machine learning (ML) in overcoming these limitations. We provide an overview of deep neural networks and their application in enhancing low-field and ultra-low-field MRI performance. Specific ML-based solutions, including advanced image reconstruction, denoising, and super-resolution algorithms, are discussed. The chapter concludes by exploring how integrating ML with low-field MRI could expand its clinical applications and improve accessibility, potentially revolutionizing its use in diverse healthcare settings.

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arXiv2024

NoSENSE: Learned unrolled cardiac MRI reconstruction without explicit sensitivity maps

We present a novel learned image reconstruction method for accelerated cardiac MRI with multiple receiver coils based on deep convolutional neural networks (CNNs) and algorithm unrolling. In contrast to many existing learned MR image reconstruction techniques that necessitate coil-sensitivity map (CSM) estimation as a distinct network component, our proposed approach avoids explicit CSM estimation. Instead, it implicitly captures and learns to exploit the inter-coil relationships of the images. Our method consists of a series of novel learned image and k-space blocks with shared latent information and adaptation to the acquisition parameters by feature-wise modulation (FiLM), as well as coil-wise data-consistency (DC) blocks. Our method achieved PSNR values of 34.89 and 35.56 and SSIM values of 0.920 and 0.942 in the cine track and mapping track validation leaderboard of the MICCAI STACOM CMRxRecon Challenge, respectively, ranking 4th among different teams at the time of writing. Code will be made available at https://github.com/fzimmermann89/CMRxRecon

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arXiv2024

PINQI: An End-to-End Physics-Informed Approach to Learned Quantitative MRI Reconstruction

Quantitative Magnetic Resonance Imaging (qMRI) enables the reproducible measurement of biophysical parameters in tissue. The challenge lies in solving a nonlinear, ill-posed inverse problem to obtain the desired tissue parameter maps from acquired raw data. While various learned and non-learned approaches have been proposed, the existing learned methods fail to fully exploit the prior knowledge about the underlying MR physics, i.e. the signal model and the acquisition model. In this paper, we propose PINQI, a novel qMRI reconstruction method that integrates the knowledge about the signal, acquisition model, and learned regularization into a single end-to-end trainable neural network. Our approach is based on unrolled alternating optimization, utilizing differentiable optimization blocks to solve inner linear and non-linear optimization tasks, as well as convolutional layers for regularization of the intermediate qualitative images and parameter maps. This design enables PINQI to leverage the advantages of both the signal model and learned regularization. We evaluate the performance of our proposed network by comparing it with recently published approaches in the context of highly undersampled $T_1$-mapping, using both a simulated brain dataset, as well as real scanner data acquired from a physical phantom and in-vivo data from healthy volunteers. The results demonstrate the superiority of our proposed solution over existing methods and highlight the effectiveness of our method in real-world scenarios.

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arXiv2024

Machine Learning for Quantitative MR Image Reconstruction

In the last years, the design of image reconstruction methods in the field of quantitative Magnetic Resonance Imaging (qMRI) has experienced a paradigm shift. Often, when dealing with (quantitative) MR image reconstruction problems, one is concerned with solving one or a couple of ill-posed inverse problems which require the use of advanced regularization methods. An increasing amount of attention is nowadays put on the development of data-driven methods using Neural Networks (NNs) to learn meaningful prior information without the need to explicitly model hand-crafted priors. In addition, the available hardware and computational resources nowadays offer the possibility to learn regularization models in a so-called model-aware fashion, which is a unique key feature that distinguishes these models from regularization methods learned in a more classical, model-agnostic manner. Model-aware methods are not only tailored to the considered data, but also to the class of considered imaging problems and nowadays constitute the state-of-the-art in image reconstruction methods. In the following chapter, we provide the reader with an extensive overview of methods that can be employed for (quantitative) MR image reconstruction, also highlighting their advantages and limitations both from a theoretical and computational point of view.

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arXiv2023

Quantitative MR Image Reconstruction using Parameter-Specific Dictionary Learning with Adaptive Dictionary-Size and Sparsity-Level Choice

Objective: We propose a method for the reconstruction of parameter-maps in Quantitative Magnetic Resonance Imaging (QMRI). Methods: Because different quantitative parameter-maps differ from each other in terms of local features, we propose a method where the employed dictionary learning (DL) and sparse coding (SC) algorithms automatically estimate the optimal dictionary-size and sparsity level separately for each parameter-map. We evaluated the method on a $T_1$-mapping QMRI problem in the brain using the BrainWeb data as well as in-vivo brain images acquired on an ultra-high field 7T scanner. We compared it to a model-based acceleration for parameter mapping (MAP) approach, other sparsity-based methods using total variation (TV), Wavelets (Wl) and Shearlets (Sh), and to a method which uses DL and SC to reconstruct qualitative images, followed by a non-linear (DL+Fit). Results: Our algorithm surpasses MAP, TV, Wl and Sh in terms of RMSE and PSNR. It yields better or comparable results to DL+Fit by additionally significantly accelerating the reconstruction by a factor of approximately seven. Conclusion: The proposed method outperforms the reported methods of comparison and yields accurate $T_1$-maps. Although presented for $T_1$-mapping in the brain, our method's structure is general and thus most probably also applicable for the the reconstruction of other quantitative parameters in other organs. Significance: From a clinical perspective, the obtained $T_1$-maps could be utilized to differentiate between healthy subjects and patients with Alzheimer's disease. From a technical perspective, the proposed unsupervised method could be employed to obtain ground-truth data for the development of data-driven methods based on supervised learning.+

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arXiv2023

Unrolled three-operator splitting for parameter-map learning in Low Dose X-ray CT reconstruction

We propose a method for fast and automatic estimation of spatially dependent regularization maps for total variation-based (TV) tomography reconstruction. The estimation is based on two distinct sub-networks, with the first sub-network estimating the regularization parameter-map from the input data while the second one unrolling T iterations of the Primal-Dual Three-Operator Splitting (PD3O) algorithm. The latter approximately solves the corresponding TV-minimization problem incorporating the previously estimated regularization parameter-map. The overall network is then trained end-to-end in a supervised learning fashion using pairs of clean-corrupted data but crucially without the need of having access to labels for the optimal regularization parameter-maps.

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arXiv2023

Learning Regularization Parameter-Maps for Variational Image Reconstruction using Deep Neural Networks and Algorithm Unrolling

We introduce a method for fast estimation of data-adapted, spatio-temporally dependent regularization parameter-maps for variational image reconstruction, focusing on total variation (TV)-minimization. Our approach is inspired by recent developments in algorithm unrolling using deep neural networks (NNs), and relies on two distinct sub-networks. The first sub-network estimates the regularization parameter-map from the input data. The second sub-network unrolls $T$ iterations of an iterative algorithm which approximately solves the corresponding TV-minimization problem incorporating the previously estimated regularization parameter-map. The overall network is trained end-to-end in a supervised learning fashion using pairs of clean-corrupted data but crucially without the need of having access to labels for the optimal regularization parameter-maps. We prove consistency of the unrolled scheme by showing that the unrolled energy functional used for the supervised learning $Γ$-converges as $T$ tends to infinity, to the corresponding functional that incorporates the exact solution map of the TV-minimization problem. We apply and evaluate our method on a variety of large scale and dynamic imaging problems in which the automatic computation of such parameters has been so far challenging: 2D dynamic cardiac MRI reconstruction, quantitative brain MRI reconstruction, low-dose CT and dynamic image denoising. The proposed method consistently improves the TV-reconstructions using scalar parameters and the obtained parameter-maps adapt well to each imaging problem and data by leading to the preservation of detailed features. Although the choice of the regularization parameter-maps is data-driven and based on NNs, the proposed algorithm is entirely interpretable since it inherits the properties of the respective iterative reconstruction method from which the network is implicitly defined.

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arXiv2022

Convolutional Dictionary Learning by End-To-End Training of Iterative Neural Networks

Sparsity-based methods have a long history in the field of signal processing and have been successfully applied to various image reconstruction problems. The involved sparsifying transformations or dictionaries are typically either pre-trained using a model which reflects the assumed properties of the signals or adaptively learned during the reconstruction - yielding so-called blind Compressed Sensing approaches. However, by doing so, the transforms are never explicitly trained in conjunction with the physical model which generates the signals. In addition, properly choosing the involved regularization parameters remains a challenging task. Another recently emerged training-paradigm for regularization methods is to use iterative neural networks (INNs) - also known as unrolled networks - which contain the physical model. In this work, we construct an INN which can be used as a supervised and physics-informed online convolutional dictionary learning algorithm. We evaluated the proposed approach by applying it to a realistic large-scale dynamic MR reconstruction problem and compared it to several other recently published works. We show that the proposed INN improves over two conventional model-agnostic training methods and yields competitive results also compared to a deep INN. Further, it does not require to choose the regularization parameters and - in contrast to deep INNs - each network component is entirely interpretable.

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arXiv2022

Convolutional Analysis Operator Learning by End-To-End Training of Iterative Neural Networks

The concept of sparsity has been extensively applied for regularization in image reconstruction. Typically, sparsifying transforms are either pre-trained on ground-truth images or adaptively trained during the reconstruction. Thereby, learning algorithms are designed to minimize some target function which encodes the desired properties of the transform. However, this procedure ignores the subsequently employed reconstruction algorithm as well as the physical model which is responsible for the image formation process. Iterative neural networks - which contain the physical model - can overcome these issues. In this work, we demonstrate how convolutional sparsifying filters can be efficiently learned by end-to-end training of iterative neural networks. We evaluated our approach on a non-Cartesian 2D cardiac cine MRI example and show that the obtained filters are better suitable for the corresponding reconstruction algorithm than the ones obtained by decoupled pre-training.

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arXiv2021

An End-To-End-Trainable Iterative Network Architecture for Accelerated Radial Multi-Coil 2D Cine MR Image Reconstruction

Purpose: Iterative Convolutional Neural Networks (CNNs) which resemble unrolled learned iterative schemes have shown to consistently deliver state-of-the-art results for image reconstruction problems across different imaging modalities. However, because these methodes include the forward model in the architecture, their applicability is often restricted to either relatively small reconstruction problems or to problems with operators which are computationally cheap to compute. As a consequence, they have so far not been applied to dynamic non-Cartesian multi-coil reconstruction problems. Methods: In this work, we propose a CNN-architecture for image reconstruction of accelerated 2D radial cine MRI with multiple receiver coils. The network is based on a computationally light CNN-component and a subsequent conjugate gradient (CG) method which can be jointly trained end-to-end using an efficient training strategy. We investigate the proposed training-strategy and compare our method to other well-known reconstruction techniques with learned and non-learned regularization methods. Results: Our proposed method outperforms all other methods based on non-learned regularization. Further, it performs similar or better than a CNN-based method employing a 3D U-Net and a method using adaptive dictionary learning. In addition, we empirically demonstrate that even by training the network with only iteration, it is possible to increase the length of the network at test time and further improve the results. Conclusions: End-to-end training allows to highly reduce the number of trainable parameters of and stabilize the reconstruction network. Further, because it is possible to change the length of the network at test time, the need to find a compromise between the complexity of the CNN-block and the number of iterations in each CG-block becomes irrelevant.

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arXiv2020

Unsupervised Adaptive Neural Network Regularization for Accelerated Radial Cine MRI

In this work, we propose an iterative reconstruction scheme (ALONE - Adaptive Learning Of NEtworks) for 2D radial cine MRI based on ground truth-free unsupervised learning of shallow convolutional neural networks. The network is trained to approximate patches of the current estimate of the solution during the reconstruction. By imposing a shallow network topology and constraining the $L_2$-norm of the learned filters, the network's representation power is limited in order not to be able to recover noise. Therefore, the network can be interpreted to perform a low dimensional approximation of the patches for stabilizing the inversion process. We compare the proposed reconstruction scheme to two ground truth-free reconstruction methods, namely a well known Total Variation (TV) minimization and an unsupervised adaptive Dictionary Learning (DIC) method. The proposed method outperforms both methods with respect to all reported quantitative measures. Further, in contrast to DIC, where the sparse approximation of the patches involves the solution of a complex optimization problem, ALONE only requires a forward pass of all patches through the shallow network and therefore significantly accelerates the reconstruction.

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arXiv2020

Neural Networks-based Regularization for Large-Scale Medical Image Reconstruction

In this paper we present a generalized Deep Learning-based approach for solving ill-posed large-scale inverse problems occuring in medical image reconstruction. Recently, Deep Learning methods using iterative neural networks and cascaded neural networks have been reported to achieve state-of-the-art results with respect to various quantitative quality measures as PSNR, NRMSE and SSIM across different imaging modalities. However, the fact that these approaches employ the forward and adjoint operators repeatedly in the network architecture requires the network to process the whole images or volumes at once, which for some applications is computationally infeasible. In this work, we follow a different reconstruction strategy by decoupling the regularization of the solution from ensuring consistency with the measured data. The regularization is given in the form of an image prior obtained by the output of a previously trained neural network which is used in a Tikhonov regularization framework. By doing so, more complex and sophisticated network architectures can be used for the removal of the artefacts or noise than it is usually the case in iterative networks. Due to the large scale of the considered problems and the resulting computational complexity of the employed networks, the priors are obtained by processing the images or volumes as patches or slices. We evaluated the method for the cases of 3D cone-beam low dose CT and undersampled 2D radial cine MRI and compared it to a total variation-minimization-based reconstruction algorithm as well as to a method with regularization based on learned overcomplete dictionaries. The proposed method outperformed all the reported methods with respect to all chosen quantitative measures and further accelerates the regularization step in the reconstruction by several orders of magnitude.

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