arXiv subjects

Mattias P. Heinrich

Publications and source records attributed to Mattias P. Heinrich.

At least 37 records · Page 2Linked to original sources

arXiv2024

The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. Quantitative evaluation and ranking were based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency analysis, and test-time instance optimization per-case basis as a post-processing step. The top-ranked method attained the MEE at or below that of the inter-rater variability for approximately 60% of the evaluated landmarks, underscoring the scope for further accuracy and robustness improvements, especially relative to human experts. The aim of BraTS-Reg is to continue to serve as an active resource for research, with the data and online evaluation tools accessible at https://bratsreg.github.io/.

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arXiv2023

Shape Matters: Detecting Vertebral Fractures Using Differentiable Point-Based Shape Decoding

Degenerative spinal pathologies are highly prevalent among the elderly population. Timely diagnosis of osteoporotic fractures and other degenerative deformities facilitates proactive measures to mitigate the risk of severe back pain and disability. In this study, we specifically explore the use of shape auto-encoders for vertebrae, taking advantage of advancements in automated multi-label segmentation and the availability of large datasets for unsupervised learning. Our shape auto-encoders are trained on a large set of vertebrae surface patches, leveraging the vast amount of available data for vertebra segmentation. This addresses the label scarcity problem faced when learning shape information of vertebrae from image intensities. Based on the learned shape features we train an MLP to detect vertebral body fractures. Using segmentation masks that were automatically generated using the TotalSegmentator, our proposed method achieves an AUC of 0.901 on the VerSe19 testset. This outperforms image-based and surface-based end-to-end trained models. Additionally, our results demonstrate that pre-training the models in an unsupervised manner enhances geometric methods like PointNet and DGCNN. Our findings emphasise the advantages of explicitly learning shape features for diagnosing osteoporotic vertebrae fractures. This approach improves the reliability of classification results and reduces the need for annotated labels. This study provides novel insights into the effectiveness of various encoder-decoder models for shape analysis of vertebrae and proposes a new decoder architecture: the point-based shape decoder.

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arXiv2023

Unsupervised 3D registration through optimization-guided cyclical self-training

State-of-the-art deep learning-based registration methods employ three different learning strategies: supervised learning, which requires costly manual annotations, unsupervised learning, which heavily relies on hand-crafted similarity metrics designed by domain experts, or learning from synthetic data, which introduces a domain shift. To overcome the limitations of these strategies, we propose a novel self-supervised learning paradigm for unsupervised registration, relying on self-training. Our idea is based on two key insights. Feature-based differentiable optimizers 1) perform reasonable registration even from random features and 2) stabilize the training of the preceding feature extraction network on noisy labels. Consequently, we propose cyclical self-training, where pseudo labels are initialized as the displacement fields inferred from random features and cyclically updated based on more and more expressive features from the learning feature extractor, yielding a self-reinforcement effect. We evaluate the method for abdomen and lung registration, consistently surpassing metric-based supervision and outperforming diverse state-of-the-art competitors. Source code is available at https://github.com/multimodallearning/reg-cyclical-self-train.

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arXiv2023

A denoised Mean Teacher for domain adaptive point cloud registration

Point cloud-based medical registration promises increased computational efficiency, robustness to intensity shifts, and anonymity preservation but is limited by the inefficacy of unsupervised learning with similarity metrics. Supervised training on synthetic deformations is an alternative but, in turn, suffers from the domain gap to the real domain. In this work, we aim to tackle this gap through domain adaptation. Self-training with the Mean Teacher is an established approach to this problem but is impaired by the inherent noise of the pseudo labels from the teacher. As a remedy, we present a denoised teacher-student paradigm for point cloud registration, comprising two complementary denoising strategies. First, we propose to filter pseudo labels based on the Chamfer distances of teacher and student registrations, thus preventing detrimental supervision by the teacher. Second, we make the teacher dynamically synthesize novel training pairs with noise-free labels by warping its moving inputs with the predicted deformations. Evaluation is performed for inhale-to-exhale registration of lung vessel trees on the public PVT dataset under two domain shifts. Our method surpasses the baseline Mean Teacher by 13.5/62.8%, consistently outperforms diverse competitors, and sets a new state-of-the-art accuracy (TRE=2.31mm). Code is available at https://github.com/multimodallearning/denoised_mt_pcd_reg.

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arXiv2023

Anatomy-guided domain adaptation for 3D in-bed human pose estimation

3D human pose estimation is a key component of clinical monitoring systems. The clinical applicability of deep pose estimation models, however, is limited by their poor generalization under domain shifts along with their need for sufficient labeled training data. As a remedy, we present a novel domain adaptation method, adapting a model from a labeled source to a shifted unlabeled target domain. Our method comprises two complementary adaptation strategies based on prior knowledge about human anatomy. First, we guide the learning process in the target domain by constraining predictions to the space of anatomically plausible poses. To this end, we embed the prior knowledge into an anatomical loss function that penalizes asymmetric limb lengths, implausible bone lengths, and implausible joint angles. Second, we propose to filter pseudo labels for self-training according to their anatomical plausibility and incorporate the concept into the Mean Teacher paradigm. We unify both strategies in a point cloud-based framework applicable to unsupervised and source-free domain adaptation. Evaluation is performed for in-bed pose estimation under two adaptation scenarios, using the public SLP dataset and a newly created dataset. Our method consistently outperforms various state-of-the-art domain adaptation methods, surpasses the baseline model by 31%/66%, and reduces the domain gap by 65%/82%. Source code is available at https://github.com/multimodallearning/da-3dhpe-anatomy.

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arXiv2022

CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation

Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.

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arXiv2022

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.

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arXiv2022

Adapting the Mean Teacher for keypoint-based lung registration under geometric domain shifts

Recent deep learning-based methods for medical image registration achieve results that are competitive with conventional optimization algorithms at reduced run times. However, deep neural networks generally require plenty of labeled training data and are vulnerable to domain shifts between training and test data. While typical intensity shifts can be mitigated by keypoint-based registration, these methods still suffer from geometric domain shifts, for instance, due to different fields of view. As a remedy, in this work, we present a novel approach to geometric domain adaptation for image registration, adapting a model from a labeled source to an unlabeled target domain. We build on a keypoint-based registration model, combining graph convolutions for geometric feature learning with loopy belief optimization, and propose to reduce the domain shift through self-ensembling. To this end, we embed the model into the Mean Teacher paradigm. We extend the Mean Teacher to this context by 1) adapting the stochastic augmentation scheme and 2) combining learned feature extraction with differentiable optimization. This enables us to guide the learning process in the unlabeled target domain by enforcing consistent predictions of the learning student and the temporally averaged teacher model. We evaluate the method for exhale-to-inhale lung CT registration under two challenging adaptation scenarios (DIR-Lab 4D CT to COPD, COPD to Learn2Reg). Our method consistently improves on the baseline model by 50%/47% while even matching the accuracy of models trained on target data. Source code is available at https://github.com/multimodallearning/registration-da-mean-teacher.

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arXiv2022

Voxelmorph++ Going beyond the cranial vault with keypoint supervision and multi-channel instance optimisation

The majority of current research in deep learning based image registration addresses inter-patient brain registration with moderate deformation magnitudes. The recent Learn2Reg medical registration benchmark has demonstrated that single-scale U-Net architectures, such as VoxelMorph that directly employ a spatial transformer loss, often do not generalise well beyond the cranial vault and fall short of state-of-the-art performance for abdominal or intra-patient lung registration. Here, we propose two straightforward steps that greatly reduce this gap in accuracy. First, we employ keypoint self-supervision with a novel network head that predicts a discretised heatmap and robustly reduces large deformations for better robustness. Second, we replace multiple learned fine-tuning steps by a single instance optimisation with hand-crafted features and the Adam optimiser. Different to other related work, including FlowNet or PDD-Net, our approach does not require a fully discretised architecture with correlation layer. Our ablation study demonstrates the importance of keypoints in both self-supervised and unsupervised (using only a MIND metric) settings. On a multi-centric inspiration-exhale lung CT dataset, including very challenging COPD scans, our method outperforms VoxelMorph by improving nonlinear alignment by 77% compared to 19% - reaching target registration errors of 2 mm that outperform all but one learning methods published to date. Extending the method to semantic features sets new stat-of-the-art performance on inter-subject abdominal CT registration.

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arXiv2021

Fast 3D registration with accurate optimisation and little learning for Learn2Reg 2021

Current approaches for deformable medical image registration often struggle to fulfill all of the following criteria: versatile applicability, small computation or training times, and the being able to estimate large deformations. Furthermore, end-to-end networks for supervised training of registration often become overly complex and difficult to train. For the Learn2Reg2021 challenge, we aim to address these issues by decoupling feature learning and geometric alignment. First, we introduce a new very fast and accurate optimisation method. By using discretised displacements and a coupled convex optimisation procedure, we are able to robustly cope with large deformations. With the help of an Adam-based instance optimisation, we achieve very accurate registration performances and by using regularisation, we obtain smooth and plausible deformation fields. Second, to be versatile for different registration tasks, we extract hand-crafted features that are modality and contrast invariant and complement them with semantic features from a task-specific segmentation U-Net. With our results we were able to achieve the overall Learn2Reg2021 challenge's second place, winning Task 1 and being second and third in the other two tasks.

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arXiv2021

Deep learning based geometric registration for medical images: How accurate can we get without visual features?

As in other areas of medical image analysis, e.g. semantic segmentation, deep learning is currently driving the development of new approaches for image registration. Multi-scale encoder-decoder network architectures achieve state-of-the-art accuracy on tasks such as intra-patient alignment of abdominal CT or brain MRI registration, especially when additional supervision, such as anatomical labels, is available. The success of these methods relies to a large extent on the outstanding ability of deep CNNs to extract descriptive visual features from the input images. In contrast to conventional methods, the explicit inclusion of geometric information plays only a minor role, if at all. In this work we take a look at an exactly opposite approach by investigating a deep learning framework for registration based solely on geometric features and optimisation. We combine graph convolutions with loopy belief message passing to enable highly accurate 3D point cloud registration. Our experimental validation is conducted on complex key-point graphs of inner lung structures, strongly outperforming dense encoder-decoder networks and other point set registration methods. Our code is publicly available at https://github.com/multimodallearning/deep-geo-reg.

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arXiv2020

Development and Characterization of a Chest CT Atlas

A major goal of lung cancer screening is to identify individuals with particular phenotypes that are associated with high risk of cancer. Identifying relevant phenotypes is complicated by the variation in body position and body composition. In the brain, standardized coordinate systems (e.g., atlases) have enabled separate consideration of local features from gross/global structure. To date, no analogous standard atlas has been presented to enable spatial mapping and harmonization in chest computational tomography (CT). In this paper, we propose a thoracic atlas built upon a large low dose CT (LDCT) database of lung cancer screening program. The study cohort includes 466 male and 387 female subjects with no screening detected malignancy (age 46-79 years, mean 64.9 years). To provide spatial mapping, we optimize a multi-stage inter-subject non-rigid registration pipeline for the entire thoracic space. We evaluate the optimized pipeline relative to two baselines with alternative non-rigid registration module: the same software with default parameters and an alternative software. We achieve a significant improvement in terms of registration success rate based on manual QA. For the entire study cohort, the optimized pipeline achieves a registration success rate of 91.7%. The application validity of the developed atlas is evaluated in terms of discriminative capability for different anatomic phenotypes, including body mass index (BMI), chronic obstructive pulmonary disease (COPD), and coronary artery calcification (CAC).

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arXiv2020

Tackling the Problem of Large Deformations in Deep Learning Based Medical Image Registration Using Displacement Embeddings

Though, deep learning based medical image registration is currently starting to show promising advances, often, it still fells behind conventional frameworks in terms of registration accuracy. This is especially true for applications where large deformations exist, such as registration of interpatient abdominal MRI or inhale-to-exhale CT lung registration. Most current works use U-Net-like architectures to predict dense displacement fields from the input images in different supervised and unsupervised settings. We believe that the U-Net architecture itself to some level limits the ability to predict large deformations (even when using multilevel strategies) and therefore propose a novel approach, where the input images are mapped into a displacement space and final registrations are reconstructed from this embedding. Experiments on inhale-to-exhale CT lung registration demonstrate the ability of our architecture to predict large deformations in a single forward path through our network (leading to errors below 2 mm).

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arXiv2020

Learning to map between ferns with differentiable binary embedding networks

Current deep learning methods are based on the repeated, expensive application of convolutions with parameter-intensive weight matrices. In this work, we present a novel concept that enables the application of differentiable random ferns in end-to-end networks. It can then be used as multiplication-free convolutional layer alternative in deep network architectures. Our experiments on the binary classification task of the TUPAC'16 challenge demonstrate improved results over the state-of-the-art binary XNOR net and only slightly worse performance than its 2x more parameter intensive floating point CNN counterpart.

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arXiv2019

Learning Deformable Point Set Registration with Regularized Dynamic Graph CNNs for Large Lung Motion in COPD Patients

Deformable registration continues to be one of the key challenges in medical image analysis. While iconic registration methods have started to benefit from the recent advances in medical deep learning, the same does not yet apply for the registration of point sets, e.g. registration based on surfaces, keypoints or landmarks. This is mainly due to the restriction of the convolution operator in modern CNNs to densely gridded input. However, with the newly developed methods from the field of geometric deep learning suitable tools are now emerging, which enable powerful analysis of medical data on irregular domains. In this work, we present a new method that enables the learning of regularized feature descriptors with dynamic graph CNNs. By incorporating the learned geometric features as prior probabilities into the well-established coherent point drift (CPD) algorithm, formulated as differentiable network layer, we establish an end-to-end framework for robust registration of two point sets. Our approach is evaluated on the challenging task of aligning keypoints extracted from lung CT scans in inhale and exhale states with large deformations and without any additional intensity information. Our results indicate that the inherent geometric structure of the extracted keypoints is sufficient to establish descriptive point features, which yield a significantly improved performance and robustness of our registration framework.

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arXiv2019

Sequential Rib Labeling and Segmentation in Chest X-Ray using Mask R-CNN

Mask R-CNN is a state-of-the-art network architecture for the detection and segmentation of object instances in the computer vision domain. In this contribution, it is used to localize, label and segment individual ribs in anterior-posterior chest X-ray images. For this purpose, several extensions have been made to the original architecture, in order to address the specific challenges of this application. This includes the use of rib specific networks, facilitating dedicated anchor boxes sampled from a training set, as well as a sequential processing of all ribs. Here, the segmentation result of the upper neighbor rib is used as additional input to the network. This approach is the first addressing both rib segmentation and anatomical labeling in chest radiographs. The results are comparable or even better than existing methods aiming only at segmentation.

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arXiv2019

Sparse Annotations with Random Walks for U-Net Segmentation of Biodegradable Bone Implants in Synchrotron Microtomograms

Currently, most bone implants used in orthopedics and traumatology are non-degradable and may need to be surgically removed later on e.g. in the case of children. This removal is associated with health risks which could be minimized by using biodegradable implants. Therefore, research on magnesium-based implants is ongoing, which can be objectively quantified through synchrotron radiation microtomography and subsequent image analysis. In order to evaluate the suitability of these materials, e.g. their stability over time, accurate pixelwise segmentations of these high-resolution scans are necessary. The fully-convolutional U-Net architecture achieves a Dice coefficient of 0.750 +/- 0.102 when trained with a small dataset with dense expert annotations. However, extending the learning to larger databases would require prohibitive annotation efforts. Hence, in this work we implemented and compared new training methods that require only a small fraction of manually annotated pixels. While directly training on these scribble annotation deteriorates the segmentation quality by 26.8 percentage points, our new random walk-based semi-automatic target achieves the same Dice overlap as a dense supervision, and thus offers a more promising approach for sparse annotations.

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arXiv2019

Closing the Gap between Deep and Conventional Image Registration using Probabilistic Dense Displacement Networks

Nonlinear image registration continues to be a fundamentally important tool in medical image analysis. Diagnostic tasks, image-guided surgery and radiotherapy as well as motion analysis all rely heavily on accurate intra-patient alignment. Furthermore, inter-patient registration enables atlas-based segmentation or landmark localisation and shape analysis. When labelled scans are scarce and anatomical differences large, conventional registration has often remained superior to deep learning methods that have so far mainly dealt with relatively small or low-complexity deformations. We address this shortcoming by leveraging ideas from probabilistic dense displacement optimisation that has excelled in many registration tasks with large deformations. We propose to design a network with approximate min-convolutions and mean field inference for differentiable displacement regularisation within a discrete weakly-supervised registration setting. By employing these meaningful and theoretically proven constraints, our learnable registration algorithm contains very few trainable weights (primarily for feature extraction) and is easier to train with few labelled scans. It is very fast in training and inference and achieves state-of-the-art accuracies for the challenging inter-patient registration of abdominal CT outperforming previous deep learning approaches by 15% Dice overlap.

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