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Medical imaging cohorts are often confounded by factors such as acquisition devices, hospital sites, patient backgrounds, and many more. As a result, deep learning models tend to learn spurious correlations instead of causally related features, limiting their generalizability to new and unseen data. This problem can be addressed by minimizing dependence measures between intermediate representations of task-related and non-task-related variables. These measures include mutual information, distance correlation, and the performance of adversarial classifiers. Here, we benchmark such dependence measures for the task of preventing shortcut learning. We study a simplified setting using Morpho-MNIST and a medical imaging task with CheXpert chest radiographs. Our results provide insights into how to mitigate confounding factors in medical imaging., Comment: Accepted to the 15th International Workshop on Machine Learning in Medical Imaging (MLMI 2024); new version: appendix moved to the end, after the references

Cardiac Cine Magnetic Resonance Imaging (MRI) provides an accurate assessment of heart morphology and function in clinical practice. However, MRI requires long acquisition times, with recent deep learning-based methods showing great promise to accelerate imaging and enhance reconstruction quality. Existing networks exhibit some common limitations that constrain further acceleration possibilities, including single-domain learning, reliance on a single regularization term, and equal feature contribution. To address these limitations, we propose to embed information from multiple domains, including low-rank, image, and k-space, in a novel deep learning network for MRI reconstruction, which we denote as A-LIKNet. A-LIKNet adopts a parallel-branch structure, enabling independent learning in the k-space and image domain. Coupled information sharing layers realize the information exchange between domains. Furthermore, we introduce attention mechanisms into the network to assign greater weights to more critical coils or important temporal frames. Training and testing were conducted on an in-house dataset, including 91 cardiovascular patients and 38 healthy subjects scanned with 2D cardiac Cine using retrospective undersampling. Additionally, we evaluated A-LIKNet on the real-time 8x prospectively undersampled data from the OCMR dataset. The results demonstrate that our proposed A-LIKNet outperforms existing methods and provides high-quality reconstructions. The network can effectively reconstruct highly retrospectively undersampled dynamic MR images up to 24x accelerations, indicating its potential for single breath-hold imaging.

Purpose: To develop an open-source and easy-to-use segmentation model that can automatically and robustly segment most major anatomical structures in MR images independently of the MR sequence. Materials and Methods: In this study we extended the capabilities of TotalSegmentator to MR images. 298 MR scans and 227 CT scans were used to segment 59 anatomical structures (20 organs, 18 bones, 11 muscles, 7 vessels, 3 tissue types) relevant for use cases such as organ volumetry, disease characterization, and surgical planning. The MR and CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, contrasts, echo times, repetition times, field strengths, slice thicknesses and sites). We trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. Results: The model showed a Dice score of 0.824 (CI: 0.801, 0.842) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed two other publicly available segmentation models (Dice score, 0.824 versus 0.762; p<0.001 and 0.762 versus 0.542; p<0.001). On the CT image test set of the original TotalSegmentator paper it almost matches the performance of the original TotalSegmentator (Dice score, 0.960 versus 0.970; p<0.001). Conclusion: Our proposed model extends the capabilities of TotalSegmentator to MR images. The annotated dataset (https://zenodo.org/doi/10.5281/zenodo.11367004) and open-source toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

Accurate motion estimation at high acceleration factors enables rapid motion-compensated reconstruction in Magnetic Resonance Imaging (MRI) without compromising the diagnostic image quality. In this work, we introduce an attention-aware deep learning-based framework that can perform non-rigid pairwise registration for fully sampled and accelerated MRI. We extract local visual representations to build similarity maps between the registered image pairs at multiple resolution levels and additionally leverage long-range contextual information using a transformer-based module to alleviate ambiguities in the presence of artifacts caused by undersampling. We combine local and global dependencies to perform simultaneous coarse and fine motion estimation. The proposed method was evaluated on in-house acquired fully sampled and accelerated data of 101 patients and 62 healthy subjects undergoing cardiac and thoracic MRI. The impact of motion estimation accuracy on the downstream task of motion-compensated reconstruction was analyzed. We demonstrate that our model derives reliable and consistent motion fields across different sampling trajectories (Cartesian and radial) and acceleration factors of up to 16x for cardiac motion and 30x for respiratory motion and achieves superior image quality in motion-compensated reconstruction qualitatively and quantitatively compared to conventional and recent deep learning-based approaches. The code is publicly available at https://github.com/lab-midas/GMARAFT., Comment: 14 pages, 7 figures

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback, Comment: 16 pages

MRI reconstruction techniques based on deep learning have led to unprecedented reconstruction quality especially in highly accelerated settings. However, deep learning techniques are also known to fail unexpectedly and hallucinate structures. This is particularly problematic if reconstructions are directly used for downstream tasks such as real-time treatment guidance or automated extraction of clinical paramters (e.g. via segmentation). Well-calibrated uncertainty quantification will be a key ingredient for safe use of this technology in clinical practice. In this paper we propose a novel probabilistic reconstruction technique (PHiRec) building on the idea of conditional hierarchical variational autoencoders. We demonstrate that our proposed method produces high-quality reconstructions as well as uncertainty quantification that is substantially better calibrated than several strong baselines. We furthermore demonstrate how uncertainties arising in the MR econstruction can be propagated to a downstream segmentation task, and show that PHiRec also allows well-calibrated estimation of segmentation uncertainties that originated in the MR reconstruction process.

In dynamic Magnetic Resonance Imaging (MRI), k-space is typically undersampled due to limited scan time, resulting in aliasing artifacts in the image domain. Hence, dynamic MR reconstruction requires not only modeling spatial frequency components in the x and y directions of k-space but also considering temporal redundancy. Most previous works rely on image-domain regularizers (priors) to conduct MR reconstruction. In contrast, we focus on interpolating the undersampled k-space before obtaining images with Fourier transform. In this work, we connect masked image modeling with k-space interpolation and propose a novel Transformer-based k-space Global Interpolation Network, termed k-GIN. Our k-GIN learns global dependencies among low- and high-frequency components of 2D+t k-space and uses it to interpolate unsampled data. Further, we propose a novel k-space Iterative Refinement Module (k-IRM) to enhance the high-frequency components learning. We evaluate our approach on 92 in-house 2D+t cardiac MR subjects and compare it to MR reconstruction methods with image-domain regularizers. Experiments show that our proposed k-space interpolation method quantitatively and qualitatively outperforms baseline methods. Importantly, the proposed approach achieves substantially higher robustness and generalizability in cases of highly-undersampled MR data. For video presentation, poster, GIF results and code please check our project page: https://jzpeterpan.github.io/k-gin.github.io/.

In cardiac CINE, motion-compensated MR reconstruction (MCMR) is an effective approach to address highly undersampled acquisitions by incorporating motion information between frames. In this work, we propose a novel perspective for addressing the MCMR problem and a more integrated and efficient solution to the MCMR field. Contrary to state-of-the-art (SOTA) MCMR methods which break the original problem into two sub-optimization problems, i.e. motion estimation and reconstruction, we formulate this problem as a single entity with one single optimization. Our approach is unique in that the motion estimation is directly driven by the ultimate goal, reconstruction, but not by the canonical motion-warping loss (similarity measurement between motion-warped images and target images). We align the objectives of motion estimation and reconstruction, eliminating the drawbacks of artifacts-affected motion estimation and therefore error-propagated reconstruction. Further, we can deliver high-quality reconstruction and realistic motion without applying any regularization/smoothness loss terms, circumventing the non-trivial weighting factor tuning. We evaluate our method on two datasets: 1) an in-house acquired 2D CINE dataset for the retrospective study and 2) the public OCMR cardiac dataset for the prospective study. The conducted experiments indicate that the proposed MCMR framework can deliver artifact-free motion estimation and high-quality MR images even for imaging accelerations up to 20x, outperforming SOTA non-MCMR and MCMR methods in both qualitative and quantitative evaluation across all experiments. The code is available at https://github.com/JZPeterPan/MCMR-Recon-Driven-Motion.

Motion-compensated MR reconstruction (MCMR) is a powerful concept with considerable potential, consisting of two coupled sub-problems: Motion estimation, assuming a known image, and image reconstruction, assuming known motion. In this work, we propose a learning-based self-supervised framework for MCMR, to efficiently deal with non-rigid motion corruption in cardiac MR imaging. Contrary to conventional MCMR methods in which the motion is estimated prior to reconstruction and remains unchanged during the iterative optimization process, we introduce a dynamic motion estimation process and embed it into the unrolled optimization. We establish a cardiac motion estimation network that leverages temporal information via a group-wise registration approach, and carry out a joint optimization between the motion estimation and reconstruction. Experiments on 40 acquired 2D cardiac MR CINE datasets demonstrate that the proposed unrolled MCMR framework can reconstruct high quality MR images at high acceleration rates where other state-of-the-art methods fail. We also show that the joint optimization mechanism is mutually beneficial for both sub-tasks, i.e., motion estimation and image reconstruction, especially when the MR image is highly undersampled.

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., Comment: To appear in IEEE Signal Processing Magazine

Physiological motion, such as cardiac and respiratory motion, during Magnetic Resonance (MR) image acquisition can cause image artifacts. Motion correction techniques have been proposed to compensate for these types of motion during thoracic scans, relying on accurate motion estimation from undersampled motion-resolved reconstruction. A particular interest and challenge lie in the derivation of reliable non-rigid motion fields from the undersampled motion-resolved data. Motion estimation is usually formulated in image space via diffusion, parametric-spline, or optical flow methods. However, image-based registration can be impaired by remaining aliasing artifacts due to the undersampled motion-resolved reconstruction. In this work, we describe a formalism to perform non-rigid registration directly in the sampled Fourier space, i.e. k-space. We propose a deep-learning based approach to perform fast and accurate non-rigid registration from the undersampled k-space data. The basic working principle originates from the Local All-Pass (LAP) technique, a recently introduced optical flow-based registration. The proposed LAPNet is compared against traditional and deep learning image-based registrations and tested on fully-sampled and highly-accelerated (with two undersampling strategies) 3D respiratory motion-resolved MR images in a cohort of 40 patients with suspected liver or lung metastases and 25 healthy subjects. The proposed LAPNet provided consistent and superior performance to image-based approaches throughout different sampling trajectories and acceleration factors.

Purpose: To introduce a novel deep learning based approach for fast and high-quality dynamic multi-coil MR reconstruction by learning a complementary time-frequency domain network that exploits spatio-temporal correlations simultaneously from complementary domains. Theory and Methods: Dynamic parallel MR image reconstruction is formulated as a multi-variable minimisation problem, where the data is regularised in combined temporal Fourier and spatial (x-f) domain as well as in spatio-temporal image (x-t) domain. An iterative algorithm based on variable splitting technique is derived, which alternates among signal de-aliasing steps in x-f and x-t spaces, a closed-form point-wise data consistency step and a weighted coupling step. The iterative model is embedded into a deep recurrent neural network which learns to recover the image via exploiting spatio-temporal redundancies in complementary domains. Results: Experiments were performed on two datasets of highly undersampled multi-coil short-axis cardiac cine MRI scans. Results demonstrate that our proposed method outperforms the current state-of-the-art approaches both quantitatively and qualitatively. The proposed model can also generalise well to data acquired from a different scanner and data with pathologies that were not seen in the training set. Conclusion: The work shows the benefit of reconstructing dynamic parallel MRI in complementary time-frequency domains with deep neural networks. The method can effectively and robustly reconstruct high-quality images from highly undersampled dynamic multi-coil data ($16 \times$ and $24 \times$ yielding 15s and 10s scan times respectively) with fast reconstruction speed (2.8s). This could potentially facilitate achieving fast single-breath-hold clinical 2D cardiac cine imaging., Comment: Accepted by Magnetic Resonance in Medicine

The concept of biological age (BA), although important in clinical practice, is hard to grasp mainly due to the lack of a clearly defined reference standard. For specific applications, especially in pediatrics, medical image data are used for BA estimation in a routine clinical context. Beyond this young age group, BA estimation is mostly restricted to whole-body assessment using non-imaging indicators such as blood biomarkers, genetic and cellular data. However, various organ systems may exhibit different aging characteristics due to lifestyle and genetic factors. Thus, a whole-body assessment of the BA does not reflect the deviations of aging behavior between organs. To this end, we propose a new imaging-based framework for organ-specific BA estimation. In this initial study, we focus mainly on brain MRI. As a first step, we introduce a chronological age (CA) estimation framework using deep convolutional neural networks (Age-Net). We quantitatively assess the performance of this framework in comparison to existing state-of-the-art CA estimation approaches. Furthermore, we expand upon Age-Net with a novel iterative data-cleaning algorithm to segregate atypical-aging patients (BA $\not \approx$ CA) from the given population. We hypothesize that the remaining population should approximate the true BA behavior. We apply the proposed methodology on a brain magnetic resonance image (MRI) dataset containing healthy individuals as well as Alzheimer's patients with different dementia ratings. We demonstrate the correlation between the predicted BAs and the expected cognitive deterioration in Alzheimer's patients. A statistical and visualization-based analysis has provided evidence regarding the potential and current challenges of the proposed methodology., Comment: Accepted to IEEE Transcations on Medical Imaging 2021. 13 pages, 14 figures, 4 tables

Purpose: To enable fast and reliable assessment of subcutaneous and visceral adipose tissue compartments derived from whole-body MRI. Methods: Quantification and localization of different adipose tissue compartments from whole-body MR images is of high interest to examine metabolic conditions. For correct identification and phenotyping of individuals at increased risk for metabolic diseases, a reliable automatic segmentation of adipose tissue into subcutaneous and visceral adipose tissue is required. In this work we propose a 3D convolutional neural network (DCNet) to provide a robust and objective segmentation. In this retrospective study, we collected 1000 cases (66$\pm$ 13 years; 523 women) from the Tuebingen Family Study and from the German Center for Diabetes research (TUEF/DZD), as well as 300 cases (53$\pm$ 11 years; 152 women) from the German National Cohort (NAKO) database for model training, validation, and testing with a transfer learning between the cohorts. These datasets had variable imaging sequences, imaging contrasts, receiver coil arrangements, scanners and imaging field strengths. The proposed DCNet was compared against a comparable 3D UNet segmentation in terms of sensitivity, specificity, precision, accuracy, and Dice overlap. Results: Fast (5-7seconds) and reliable adipose tissue segmentation can be obtained with high Dice overlap (0.94), sensitivity (96.6%), specificity (95.1%), precision (92.1%) and accuracy (98.4%) from 3D whole-body MR datasets (field of view coverage 450x450x2000mm${}^3$). Segmentation masks and adipose tissue profiles are automatically reported back to the referring physician. Conclusion: Automatic adipose tissue segmentation is feasible in 3D whole-body MR data sets and is generalizable to different epidemiological cohort studies with the proposed DCNet., Comment: This manuscript has been accepted for publication in Radiology: Artificial Intelligence (https://pubs.rsna.org/journal/ai), which is published by the Radiological Society of North America (RSNA)

Individuals age differently depending on a multitude of different factors such as lifestyle, medical history and genetics. Often, the global chronological age is not indicative of the true ageing process. An organ-based age estimation would yield a more accurate health state assessment. In this work, we propose a new deep learning architecture for organ-based age estimation based on magnetic resonance images (MRI). The proposed network is a 3D convolutional neural network (CNN) with increased depth and width made possible by the hybrid utilization of inception and fire modules. We apply the proposed framework for the tasks of brain and knee age estimation. Quantitative comparisons against concurrent MR-based regression networks and different 2D and 3D data feeding strategies illustrated the superior performance of the proposed work., Comment: Submitted to IEEE EUSIPCO 2020

Motion is one of the main sources for artifacts in magnetic resonance (MR) images. It can have significant consequences on the diagnostic quality of the resultant scans. Previously, supervised adversarial approaches have been suggested for the correction of MR motion artifacts. However, these approaches suffer from the limitation of required paired co-registered datasets for training which are often hard or impossible to acquire. Building upon our previous work, we introduce a new adversarial framework with a new generator architecture and loss function for the unsupervised correction of severe rigid motion artifacts in the brain region. Quantitative and qualitative comparisons with other supervised and unsupervised translation approaches showcase the enhanced performance of the introduced framework., Comment: Submitted to IEEE ISBI 2020

Image-to-image translation is a new field in computer vision with multiple potential applications in the medical domain. However, for supervised image translation frameworks, co-registered datasets, paired in a pixel-wise sense, are required. This is often difficult to acquire in realistic medical scenarios. On the other hand, unsupervised translation frameworks often result in blurred translated images with unrealistic details. In this work, we propose a new unsupervised translation framework which is titled Cycle-MedGAN. The proposed framework utilizes new non-adversarial cycle losses which direct the framework to minimize the textural and perceptual discrepancies in the translated images. Qualitative and quantitative comparisons against other unsupervised translation approaches demonstrate the performance of the proposed framework for PET-CT translation and MR motion correction., Comment: Submitted to EUSIPCO 2019, 5 pages

Motion artifacts are a primary source of magnetic resonance (MR) image quality deterioration with strong repercussions on diagnostic performance. Currently, MR motion correction is carried out either prospectively, with the help of motion tracking systems, or retrospectively by mainly utilizing computationally expensive iterative algorithms. In this paper, we utilize a new adversarial framework, titled MedGAN, for the joint retrospective correction of rigid and non-rigid motion artifacts in different body regions and without the need for a reference image. MedGAN utilizes a unique combination of non-adversarial losses and a new generator architecture to capture the textures and fine-detailed structures of the desired artifact-free MR images. Quantitative and qualitative comparisons with other adversarial techniques have illustrated the proposed model performance., Comment: 5 pages, 2 figures, under review for the IEEE International Symposium for Biomedical Images

Magnetic resonance (MR) imaging offers a wide variety of imaging techniques. A large amount of data is created per examination which needs to be checked for sufficient quality in order to derive a meaningful diagnosis. This is a manual process and therefore time- and cost-intensive. Any imaging artifacts originating from scanner hardware, signal processing or induced by the patient may reduce the image quality and complicate the diagnosis or any image post-processing. Therefore, the assessment or the ensurance of sufficient image quality in an automated manner is of high interest. Usually no reference image is available or difficult to define. Therefore, classical reference-based approaches are not applicable. Model observers mimicking the human observers (HO) can assist in this task. Thus, we propose a new machine-learning-based reference-free MR image quality assessment framework which is trained on HO-derived labels to assess MR image quality immediately after each acquisition. We include the concept of active learning and present an efficient blinded reading platform to reduce the effort in the HO labeling procedure. Derived image features and the applied classifiers (support-vector-machine, deep neural network) are investigated for a cohort of 250 patients. The MR image quality assessment framework can achieve a high test accuracy of 93.7$\%$ for estimating quality classes on a 5-point Likert-scale. The proposed MR image quality assessment framework is able to provide an accurate and efficient quality estimation which can be used as a prospective quality assurance including automatic acquisition adaptation or guided MR scanner operation, and/or as a retrospective quality assessment including support of diagnostic decisions or quality control in cohort studies.

Image-to-image translation is considered a new frontier in the field of medical image analysis, with numerous potential applications. However, a large portion of recent approaches offers individualized solutions based on specialized task-specific architectures or require refinement through non-end-to-end training. In this paper, we propose a new framework, named MedGAN, for medical image-to-image translation which operates on the image level in an end-to-end manner. MedGAN builds upon recent advances in the field of generative adversarial networks (GANs) by merging the adversarial framework with a new combination of non-adversarial losses. We utilize a discriminator network as a trainable feature extractor which penalizes the discrepancy between the translated medical images and the desired modalities. Moreover, style-transfer losses are utilized to match the textures and fine-structures of the desired target images to the translated images. Additionally, we present a new generator architecture, titled CasNet, which enhances the sharpness of the translated medical outputs through progressive refinement via encoder-decoder pairs. Without any application-specific modifications, we apply MedGAN on three different tasks: PET-CT translation, correction of MR motion artefacts and PET image denoising. Perceptual analysis by radiologists and quantitative evaluations illustrate that the MedGAN outperforms other existing translation approaches., Comment: 16 pages, 8 figures