A Coarse-to-Fine Deformable Transformation Framework for Unsupervised Multi-Contrast MR Image Registration with Dual Consistency Constraint

Anatomically plausible segmentations: Explicitly preserving topology through prior deformations

Since the rise of deep learning, new medical segmentation methods have rapidly been proposed with extremely promising results, often reporting marginal improvements on the previous state-of-the-art (SOTA) method. However, on visual inspection errors are often revealed, such as topological mistakes (e.g. holes or folds), that are not detected using traditional evaluation metrics. Incorrect topology can often lead to errors in clinically required downstream image processing tasks. Therefore, there is a need for new methods to focus on ensuring segmentations are topologically correct. In this work, we present TEDS-Net: a segmentation network that preserves anatomical topology whilst maintaining segmentation performance that is competitive with SOTA baselines. Further, we show how current SOTA segmentation methods can introduce problematic topological errors. TEDS-Net achieves anatomically plausible segmentation by using learnt topology-preserving fields to deform a prior. Traditionally, topology-preserving fields are described in the continuous domain and begin to break down when working in the discrete domain. Here, we introduce additional modifications that more strictly enforce topology preservation. We illustrate our method on an open-source medical heart dataset, performing both single and multi-structure segmentation, and show that the generated fields contain no folding voxels, which corresponds to full topology preservation on individual structures whilst vastly outperforming the other baselines on overall scene topology. The code is available at: https://github.com/mwyburd/TEDS-Net.

Affine medical image registration with fusion feature mapping in local and global

Objective. Medical image affine registration is a crucial basis before using deformable registration. On the one hand, the traditional affine registration methods based on step-by-step optimization are very time-consuming, so these methods are not compatible with most real-time medical applications. On the other hand, convolutional neural networks are limited in modeling long-range spatial relationships of the features due to inductive biases, such as weight sharing and locality. This is not conducive to affine registration tasks. Therefore, the evolution of real-time and high-accuracy affine medical image registration algorithms is necessary for registration applications.Approach. In this paper, we propose a deep learning-based coarse-to-fine global and local feature fusion architecture for fast affine registration, and we use an unsupervised approach for end-to-end training. We use multiscale convolutional kernels as our elemental convolutional blocks to enhance feature extraction. Then, to learn the long-range spatial relationships of the features, we propose a new affine registration framework with weighted global positional attention that fuses global feature mapping and local feature mapping. Moreover, the fusion regressor is designed to generate the affine parameters.Main results. The additive fusion method can be adaptive to global mapping and local mapping, which improves affine registration accuracy without the center of mass initialization. In addition, the max pooling layer and the multiscale convolutional kernel coding module increase the ability of the model in affine registration.Significance. We validate the effectiveness of our method on the OASIS dataset with 414 3D MRI brain maps. Comprehensive results demonstrate that our method achieves state-of-the-art affine registration accuracy and very efficient runtimes.

Collaborative Learning for Annotation-Efficient Volumetric MR Image Segmentation

BACKGROUND

Deep learning has presented great potential in accurate MR image segmentation when enough labeled data are provided for network optimization. However, manually annotating three-dimensional (3D) MR images is tedious and time-consuming, requiring experts with rich domain knowledge and experience.

PURPOSE

To build a deep learning method exploring sparse annotations, namely only a single two-dimensional slice label for each 3D training MR image.

STUDY TYPE

Retrospective.

POPULATION

Three-dimensional MR images of 150 subjects from two publicly available datasets were included. Among them, 50 (1377 image slices) are for prostate segmentation. The other 100 (8800 image slices) are for left atrium segmentation. Five-fold cross-validation experiments were carried out utilizing the first dataset. For the second dataset, 80 subjects were used for training and 20 were used for testing.

FIELD STRENGTH/SEQUENCE

1.5 T and 3.0 T; axial T2-weighted and late gadolinium-enhanced, 3D respiratory navigated, inversion recovery prepared gradient echo pulse sequence.

ASSESSMENT

A collaborative learning method by integrating the strengths of semi-supervised and self-supervised learning schemes was developed. The method was trained using labeled central slices and unlabeled noncentral slices. Segmentation performance on testing set was reported quantitatively and qualitatively.

STATISTICAL TESTS

Quantitative evaluation metrics including boundary intersection-over-union (B-IoU), Dice similarity coefficient, average symmetric surface distance, and relative absolute volume difference were calculated. Paired t test was performed, and P < 0.05 was considered statistically significant.

RESULTS

Compared to fully supervised training with only the labeled central slice, mean teacher, uncertainty-aware mean teacher, deep co-training, interpolation consistency training (ICT), and ambiguity-consensus mean teacher, the proposed method achieved a substantial improvement in segmentation accuracy, increasing the mean B-IoU significantly by more than 10.0% for prostate segmentation (proposed method B-IoU: 70.3% ± 7.6% vs. ICT B-IoU: 60.3% ± 11.2%) and by more than 6.0% for left atrium segmentation (proposed method B-IoU: 66.1% ± 6.8% vs. ICT B-IoU: 60.1% ± 7.1%).

DATA CONCLUSIONS

A collaborative learning method trained using sparse annotations can segment prostate and left atrium with high accuracy.

LEVEL OF EVIDENCE

0 TECHNICAL EFFICACY: Stage 1.

Sparse annotation learning for dense volumetric MR image segmentation with uncertainty estimation

Objective.Training neural networks for pixel-wise or voxel-wise image segmentation is a challenging task that requires a considerable amount of training samples with highly accurate and densely delineated ground truth maps. This challenge becomes especially prominent in the medical imaging domain, where obtaining reliable annotations for training samples is a difficult, time-consuming, and expert-dependent process. Therefore, developing models that can perform well under the conditions of limited annotated training data is desirable.Approach.In this study, we propose an innovative framework called the extremely sparse annotation neural network (ESA-Net) that learns with only the single central slice label for 3D volumetric segmentation which explores both intra-slice pixel dependencies and inter-slice image correlations with uncertainty estimation. Specifically, ESA-Net consists of four specially designed distinct components: (1) an intra-slice pixel dependency-guided pseudo-label generation module that exploits uncertainty in network predictions while generating pseudo-labels for unlabeled slices with temporal ensembling; (2) an inter-slice image correlation-constrained pseudo-label propagation module which propagates labels from the labeled central slice to unlabeled slices by self-supervised registration with rotation ensembling; (3) a pseudo-label fusion module that fuses the two sets of generated pseudo-labels with voxel-wise uncertainty guidance; and (4) a final segmentation network optimization module to make final predictions with scoring-based label quantification.Main results.Extensive experimental validations have been performed on two popular yet challenging magnetic resonance image segmentation tasks and compared to five state-of-the-art methods.Significance.Results demonstrate that our proposed ESA-Net can consistently achieve better segmentation performances even under the extremely sparse annotation setting, highlighting its effectiveness in exploiting information from unlabeled data.

EDIRNet: an unsupervised deformable registration model for X-ray and neutron images

For high-precision industrial non-destructive testing, multimodal image registration technology can be employed to register X-ray and neutron images. X-ray and neutron image registration algorithms usually use conventional methods through iterative optimization. These methods will increase the cost of registration time and require more initialization parameters. The imaging results of internal sample structures can suffer from edge blurring due to the influence of a neutron beam collimator aperture, X-ray focal point, and imaging angles. We present an unsupervised learning model, EDIRNet, based on deep learning for deformable registration of X-ray and neutron images. We define the registration process as a function capable of estimating the flow field from input images. By leveraging deep learning techniques, we effectively parameterize this function. Consequently, given a registration image, our optimized network parameters enable rapid and direct estimation of the flow field between the images. We design an attention-based edge enhancement module to enhance the edge features of the image. For evaluating our presented network model, we utilize a dataset including 552 pairs of X-ray and neutron images. The experimental results show that the registration accuracy of EDIRNet reaches 93.09%. Compared with traditional algorithms, the accuracy of EDIRNet is improved by 3.17%, and the registration time is reduced by 28.75 s.

Deformable medical image registration with global-local transformation network and region similarity constraint

Deformable medical image registration can achieve fast and accurate alignment between two images, enabling medical professionals to analyze images of different subjects in a unified anatomical space. As such, it plays an important role in many medical image studies. Current deep learning (DL)-based approaches for image registration directly learn spatial transformation from one image to another, relying on a convolutional neural network and ground truth or similarity metrics. However, these methods only use a global similarity energy function to evaluate the similarity of a pair of images, which ignores the similarity of regions of interest (ROIs) within the images. This can limit the accuracy of the image registration and affect the analysis of specific ROIs. Additionally, DL-based methods often estimate global spatial transformations of images directly, without considering local spatial transformations of ROIs within the images. To address this issue, we propose a novel global-local transformation network with a region similarity constraint that maximizes the similarity of ROIs within the images and estimates both global and local spatial transformations simultaneously. Experiments conducted on four public 3D MRI datasets demonstrate that the proposed method achieves the highest registration performance in terms of accuracy and generalization compared to other state-of-the-art methods.

Weakly supervised volumetric prostate registration for MRI-TRUS image driven by signed distance map

Image registration is a fundamental step for MRI-TRUS fusion targeted biopsy. Due to the inherent representational differences between these two image modalities, though, intensity-based similarity losses for registration tend to result in poor performance. To mitigate this, comparison of organ segmentations, functioning as a weak proxy measure of image similarity, has been proposed. Segmentations, though, are limited in their information encoding capabilities. Signed distance maps (SDMs), on the other hand, encode these segmentations into a higher dimensional space where shape and boundary information are implicitly captured, and which, in addition, yield high gradients even for slight mismatches, thus preventing vanishing gradients during deep-network training. Based on these advantages, this study proposes a weakly-supervised deep learning volumetric registration approach driven by a mixed loss that operates both on segmentations and their corresponding SDMs, and which is not only robust to outliers, but also encourages optimal global alignment. Our experimental results, performed on a public prostate MRI-TRUS biopsy dataset, demonstrate that our method outperforms other weakly-supervised registration approaches with a dice similarity coefficient (DSC), Hausdorff distance (HD) and mean surface distance (MSD) of 87.3 ± 11.3, 4.56 ± 1.95 mm, and 0.053 ± 0.026 mm, respectively. We also show that the proposed method effectively preserves the prostate gland's internal structure.

Normal vibration distribution search-based differential evolution algorithm for multimodal biomedical image registration

In linear registration, a floating image is spatially aligned with a reference image after performing a series of linear metric transformations. Additionally, linear registration is mainly considered a preprocessing version of nonrigid registration. To better accomplish the task of finding the optimal transformation in pairwise intensity-based medical image registration, in this work, we present an optimization algorithm called the normal vibration distribution search-based differential evolution algorithm (NVSA), which is modified from the Bernstein search-based differential evolution (BSD) algorithm. We redesign the search pattern of the BSD algorithm and import several control parameters as part of the fine-tuning process to reduce the difficulty of the algorithm. In this study, 23 classic optimization functions and 16 real-world patients (resulting in 41 multimodal registration scenarios) are used in experiments performed to statistically investigate the problem solving ability of the NVSA. Nine metaheuristic algorithms are used in the conducted experiments. When compared to the commonly utilized registration methods, such as ANTS, Elastix, and FSL, our method achieves better registration performance on the RIRE dataset. Moreover, we prove that our method can perform well with or without its initial spatial transformation in terms of different evaluation indicators, demonstrating its versatility and robustness for various clinical needs and applications. This study establishes the idea that metaheuristic-based methods can better accomplish linear registration tasks than the frequently used approaches; the proposed method demonstrates promise that it can solve real-world clinical and service problems encountered during nonrigid registration as a preprocessing approach.The source code of the NVSA is publicly available at https://github.com/PengGui-N/NVSA.

A ready-to-use machine learning tool for symmetric multi-modality registration of brain MRI

Volumetric registration of brain MRI is routinely used in human neuroimaging, e.g., to align different MRI modalities, to measure change in longitudinal analysis, to map an individual to a template, or in registration-based segmentation. Classical registration techniques based on numerical optimization have been very successful in this domain, and are implemented in widespread software suites like ANTs, Elastix, NiftyReg, or DARTEL. Over the last 7-8 years, learning-based techniques have emerged, which have a number of advantages like high computational efficiency, potential for higher accuracy, easy integration of supervision, and the ability to be part of a meta-architectures. However, their adoption in neuroimaging pipelines has so far been almost inexistent. Reasons include: lack of robustness to changes in MRI modality and resolution; lack of robust affine registration modules; lack of (guaranteed) symmetry; and, at a more practical level, the requirement of deep learning expertise that may be lacking at neuroimaging research sites. Here, we present EasyReg, an open-source, learning-based registration tool that can be easily used from the command line without any deep learning expertise or specific hardware. EasyReg combines the features of classical registration tools, the capabilities of modern deep learning methods, and the robustness to changes in MRI modality and resolution provided by our recent work in domain randomization. As a result, EasyReg is: fast; symmetric; diffeomorphic (and thus invertible); agnostic to MRI modality and resolution; compatible with affine and nonlinear registration; and does not require any preprocessing or parameter tuning. We present results on challenging registration tasks, showing that EasyReg is as accurate as classical methods when registering 1 mm isotropic scans within MRI modality, but much more accurate across modalities and resolutions. EasyReg is publicly available as part of FreeSurfer; see https://surfer.nmr.mgh.harvard.edu/fswiki/EasyReg .

Topologically preserved registration of 3D CT images with deep networks

Objective. Computed Tomography (CT) image registration makes fast and accurate imaging-based disease diagnosis possible. We aim to develop a framework which can perform accurate local registration of organs in 3D CT images while preserving the topology of transformation.Approach. In this framework, the Faster R-CNN method is first used to detect local areas containing organs from fixed and moving images whose results are then registered with a weakly supervised deep neural network. In this network, a novel 3D channel coordinate attention (CA) module is introduced to reduce the loss of position information. The image edge loss and the organ labelling loss are used to weakly supervise the training process of our deep network, which enables the network learning to focus on registering organs and image structures. An intuitive inverse module is also used to reduce the folding of deformation field. More specifically, the folding is suppressed directly by simultaneously maximizing forward and backward registration accuracy in the image domain rather than indirectly by measuring the consistency of forward and inverse deformation fields as usual.Main results. Our method achieves an average dice similarity coefficient (DSC) of 0.954 and an average Similarity (Sim) of 0.914 on publicly available liver datasets (LiTS for training and Sliver07 for testing) and achieves an average DSC of 0.914 and an average Sim of 0.947 on our home-built left ventricular myocardium (LVM) dataset.Significance. Experimental results show that our proposed method can significantly improve the registration accuracy of organs such as the liver and LVM. Moreover, our inverse module can intuitively improve the inherent topological preservation of transformations.

Development and Application of a Standardized Testset for an Artificial Intelligence Medical Device Intended for the Computer-Aided Diagnosis of Diabetic Retinopathy

Objective

To explore a centralized approach to build test sets and assess the performance of an artificial intelligence medical device (AIMD) which is intended for computer-aided diagnosis of diabetic retinopathy (DR).

Method

A framework was proposed to conduct data collection, data curation, and annotation. Deidentified colour fundus photographs were collected from 11 partner hospitals with raw labels. Photographs with sensitive information or authenticity issues were excluded during vetting. A team of annotators was recruited through qualification examinations and trained. The annotation process included three steps: initial annotation, review, and arbitration. The annotated data then composed a standardized test set, which was further imported to algorithms under test (AUT) from different developers. The algorithm outputs were compared with the final annotation results (reference standard).

Result

The test set consists of 6327 digital colour fundus photographs. The final labels include 5 stages of DR and non-DR, as well as other ocular diseases and photographs with unacceptable quality. The Fleiss Kappa was 0.75 among the annotators. The Cohen's kappa between raw labels and final labels is 0.5. Using this test set, five AUTs were tested and compared quantitatively. The metrics include accuracy, sensitivity, and specificity. The AUTs showed inhomogeneous capabilities to classify different types of fundus photographs.

Conclusions

This article demonstrated a workflow to build standardized test sets and conduct algorithm testing of the AIMD for computer-aided diagnosis of diabetic retinopathy. It may provide a reference to develop technical standards that promote product verification and quality control, improving the comparability of products.

A review of deep learning-based deformable medical image registration

The alignment of images through deformable image registration is vital to clinical applications (e.g., atlas creation, image fusion, and tumor targeting in image-guided navigation systems) and is still a challenging problem. Recent progress in the field of deep learning has significantly advanced the performance of medical image registration. In this review, we present a comprehensive survey on deep learning-based deformable medical image registration methods. These methods are classified into five categories: Deep Iterative Methods, Supervised Methods, Unsupervised Methods, Weakly Supervised Methods, and Latest Methods. A detailed review of each category is provided with discussions about contributions, tasks, and inadequacies. We also provide statistical analysis for the selected papers from the point of view of image modality, the region of interest (ROI), evaluation metrics, and method categories. In addition, we summarize 33 publicly available datasets that are used for benchmarking the registration algorithms. Finally, the remaining challenges, future directions, and potential trends are discussed in our review.

CDFRegNet: A cross-domain fusion registration network for CT-to-CBCT image registration

BACKGROUND AND OBJECTIVE

Computer tomography (CT) to cone-beam computed tomography (CBCT) image registration plays an important role in radiotherapy treatment placement, dose verification, and anatomic changes monitoring during radiotherapy. However, fast and accurate CT-to-CBCT image registration is still very challenging due to the intensity differences, the poor image quality of CBCT images, and inconsistent structure information.

METHODS

To address these problems, a novel unsupervised network named cross-domain fusion registration network (CDFRegNet) is proposed. First, a novel edge-guided attention module (EGAM) is designed, aiming at capturing edge information based on the gradient prior images and guiding the network to model the spatial correspondence between two image domains. Moreover, a novel cross-domain attention module (CDAM) is proposed to improve the network's ability to guide the network to effectively map and fuse the domain-specific features.

RESULTS

Extensive experiments on a real clinical dataset were carried out, and the experimental results verify that the proposed CDFRegNet can register CT to CBCT images effectively and obtain the best performance, while compared with other representative methods, with a mean DSC of 80.01±7.16%, a mean TRE of 2.27±0.62 mm, and a mean MHD of 1.50±0.32 mm. The ablation experiments also proved that our EGAM and CDAM can further improve the accuracy of the registration network and they can generalize well to other registration networks.

CONCLUSION

This paper proposed a novel CT-to-CBCT registration method based on EGAM and CDAM, which has the potential to improve the accuracy of multi-domain image registration.

Artificial intelligence in multi-parametric magnetic resonance imaging: A review

Multi-parametric magnetic resonance imaging (mpMRI) is an indispensable tool in the clinical workflow for the diagnosis and treatment planning of various diseases. Machine learning-based artificial intelligence (AI) methods, especially those adopting the deep learning technique, have been extensively employed to perform mpMRI image classification, segmentation, registration, detection, reconstruction, and super-resolution. The current availability of increasing computational power and fast-improving AI algorithms have empowered numerous computer-based systems for applying mpMRI to disease diagnosis, imaging-guided radiotherapy, patient risk and overall survival time prediction, and the development of advanced quantitative imaging technology for magnetic resonance fingerprinting. However, the wide application of these developed systems in the clinic is still limited by a number of factors, including robustness, reliability, and interpretability. This survey aims to provide an overview for new researchers in the field as well as radiologists with the hope that they can understand the general concepts, main application scenarios, and remaining challenges of AI in mpMRI. This article is protected by copyright. All rights reserved.

Multimodal Remote Sensing Image Registration Methods and Advancements: A Survey

With rapid advancements in remote sensing image registration algorithms, comprehensive imaging applications are no longer limited to single-modal remote sensing images. Instead, multi-modal remote sensing (MMRS) image registration has become a research focus in recent years. However, considering multi-source, multi-temporal, and multi-spectrum input introduces significant nonlinear radiation differences in MMRS images for which researchers need to develop novel solutions. At present, comprehensive reviews and analyses of MMRS image registration methods are inadequate in related fields. Thus, this paper introduces three theoretical frameworks: namely, area-based, feature-based and deep learning-based methods. We present a brief review of traditional methods and focus on more advanced methods for MMRS image registration proposed in recent years. Our review or comprehensive analysis is intended to provide researchers in related fields with advanced understanding to achieve further breakthroughs and innovations.