Junyu Chen

Se-In Jang, Tinsu Pan, Ye Li et al.

Position emission tomography (PET) is widely used in clinics and research due to its quantitative merits and high sensitivity, but suffers from low signal-to-noise ratio (SNR). Recently convolutional neural networks (CNNs) have been widely used to improve PET image quality. Though successful and efficient in local feature extraction, CNN cannot capture long-range dependencies well due to its limited receptive field. Global multi-head self-attention (MSA) is a popular approach to capture long-range information. However, the calculation of global MSA for 3D images has high computational costs. In this work, we proposed an efficient spatial and channel-wise encoder-decoder transformer, Spach Transformer, that can leverage spatial and channel information based on local and global MSAs. Experiments based on datasets of different PET tracers, i.e., $^{18}$F-FDG, $^{18}$F-ACBC, $^{18}$F-DCFPyL, and $^{68}$Ga-DOTATATE, were conducted to evaluate the proposed framework. Quantitative results show that the proposed Spach Transformer framework outperforms state-of-the-art deep learning architectures. Our codes are available at https://github.com/sijang/SpachTransformer

Junyu Chen, Yihao Liu, Shuwen Wei et al.

Deep learning technologies have dramatically reshaped the field of medical image registration over the past decade. The initial developments, such as regression-based and U-Net-based networks, established the foundation for deep learning in image registration. Subsequent progress has been made in various aspects of deep learning-based registration, including similarity measures, deformation regularizations, network architectures, and uncertainty estimation. These advancements have not only enriched the field of image registration but have also facilitated its application in a wide range of tasks, including atlas construction, multi-atlas segmentation, motion estimation, and 2D-3D registration. In this paper, we present a comprehensive overview of the most recent advancements in deep learning-based image registration. We begin with a concise introduction to the core concepts of deep learning-based image registration. Then, we delve into innovative network architectures, loss functions specific to registration, and methods for estimating registration uncertainty. Additionally, this paper explores appropriate evaluation metrics for assessing the performance of deep learning models in registration tasks. Finally, we highlight the practical applications of these novel techniques in medical imaging and discuss the future prospects of deep learning-based image registration.

Jun Li, Junyu Chen, Yucheng Tang et al.

Transformer, the latest technological advance of deep learning, has gained prevalence in natural language processing or computer vision. Since medical imaging bear some resemblance to computer vision, it is natural to inquire about the status quo of Transformers in medical imaging and ask the question: can the Transformer models transform medical imaging? In this paper, we attempt to make a response to the inquiry. After a brief introduction of the fundamentals of Transformers, especially in comparison with convolutional neural networks (CNNs), and highlighting key defining properties that characterize the Transformers, we offer a comprehensive review of the state-of-the-art Transformer-based approaches for medical imaging and exhibit current research progresses made in the areas of medical image segmentation, recognition, detection, registration, reconstruction, enhancement, etc. In particular, what distinguishes our review lies in its organization based on the Transformer's key defining properties, which are mostly derived from comparing the Transformer and CNN, and its type of architecture, which specifies the manner in which the Transformer and CNN are combined, all helping the readers to best understand the rationale behind the reviewed approaches. We conclude with discussions of future perspectives.

Zhangxing Bian, Shuwen Wei, Yihao Liu et al.

Tagged magnetic resonance imaging (tMRI) has been employed for decades to measure the motion of tissue undergoing deformation. However, registration-based motion estimation from tMRI is difficult due to the periodic patterns in these images, particularly when the motion is large. With a larger motion the registration approach gets trapped in a local optima, leading to motion estimation errors. We introduce a novel "momenta, shooting, and correction" framework for Lagrangian motion estimation in the presence of repetitive patterns and large motion. This framework, grounded in Lie algebra and Lie group principles, accumulates momenta in the tangent vector space and employs exponential mapping in the diffeomorphic space for rapid approximation towards true optima, circumventing local optima. A subsequent correction step ensures convergence to true optima. The results on a 2D synthetic dataset and a real 3D tMRI dataset demonstrate our method's efficiency in estimating accurate, dense, and diffeomorphic 2D/3D motion fields amidst large motion and repetitive patterns.

Ye Li, Jianan Cui, Junyu Chen et al.

In PET, the amount of relative (signal-dependent) noise present in different body regions can be significantly different and is inherently related to the number of counts present in that region. The number of counts in a region depends, in principle and among other factors, on the total administered activity, scanner sensitivity, image acquisition duration, radiopharmaceutical tracer uptake in the region, and patient local body morphometry surrounding the region. In theory, less amount of denoising operations is needed to denoise a high-count (low relative noise) image than images a low-count (high relative noise) image, and vice versa. The current deep-learning-based methods for PET image denoising are predominantly trained on image appearance only and have no special treatment for images of different noise levels. Our hypothesis is that by explicitly providing the local relative noise level of the input image to a deep convolutional neural network (DCNN), the DCNN can outperform itself trained on image appearance only. To this end, we propose a noise-level-aware framework denoising framework that allows embedding of local noise level into a DCNN. The proposed is trained and tested on 30 and 15 patient PET images acquired on a GE Discovery MI PET/CT system. Our experiments showed that the increases in both PSNR and SSIM from our backbone network with relative noise level embedding (NLE) versus the same network without NLE were statistically significant with p<0.001, and the proposed method significantly outperformed a strong baseline method by a large margin.

Junyu Chen, Yihao Liu, Yufan He et al.

Transformers have recently shown promise for medical image applications, leading to an increasing interest in developing such models for medical image registration. Recent advancements in designing registration Transformers have focused on using cross-attention (CA) to enable a more precise understanding of spatial correspondences between moving and fixed images. Here, we propose a novel CA mechanism that computes windowed attention using deformable windows. In contrast to existing CA mechanisms that require intensive computational complexity by either computing CA globally or locally with a fixed and expanded search window, the proposed deformable CA can selectively sample a diverse set of features over a large search window while maintaining low computational complexity. The proposed model was extensively evaluated on multi-modal, mono-modal, and atlas-to-patient registration tasks, demonstrating promising performance against state-of-the-art methods and indicating its effectiveness for medical image registration. The source code for this work will be available after publication.

Junyu Chen, Yihao Liu, Yufan He et al.

In the past, optimization-based registration models have used spatially-varying regularization to account for deformation variations in different image regions. However, deep learning-based registration models have mostly relied on spatially-invariant regularization. Here, we introduce an end-to-end framework that uses neural networks to learn a spatially-varying deformation regularizer directly from data. The hyperparameter of the proposed regularizer is conditioned into the network, enabling easy tuning of the regularization strength. The proposed method is built upon a Transformer-based model, but it can be readily adapted to any network architecture. We thoroughly evaluated the proposed approach using publicly available datasets and observed a significant performance improvement while maintaining smooth deformation. The source code of this work will be made available after publication.

Zifan Wang, Zhuorui Ye, Haoran Wu et al.

We study a new problem of semantic complete scene forecasting (SCSF) in this work. Given a 4D dynamic point cloud sequence, our goal is to forecast the complete scene corresponding to the future next frame along with its semantic labels. To tackle this challenging problem, we properly model the synergetic relationship between future forecasting and semantic scene completion through a novel network named SCSFNet. SCSFNet leverages a hybrid geometric representation for high-resolution complete scene forecasting. To leverage multi-frame observation as well as the understanding of scene dynamics to ease the completion task, SCSFNet introduces an attention-based skip connection scheme. To ease the need to model occlusion variations and to better focus on the occluded part, SCSFNet utilizes auxiliary visibility grids to guide the forecasting task. To evaluate the effectiveness of SCSFNet, we conduct experiments on various benchmarks including two large-scale indoor benchmarks we contributed and the outdoor SemanticKITTI benchmark. Extensive experiments show SCSFNet outperforms baseline methods on multiple metrics by a large margin, and also prove the synergy between future forecasting and semantic scene completion.

Zhangxing Bian, Ahmed Alshareef, Shuwen Wei et al.

Magnetic Resonance Imaging with tagging (tMRI) has long been utilized for quantifying tissue motion and strain during deformation. However, a phenomenon known as tag fading, a gradual decrease in tag visibility over time, often complicates post-processing. The first contribution of this study is to model tag fading by considering the interplay between $T_1$ relaxation and the repeated application of radio frequency (RF) pulses during serial imaging sequences. This is a factor that has been overlooked in prior research on tMRI post-processing. Further, we have observed an emerging trend of utilizing raw tagged MRI within a deep learning-based (DL) registration framework for motion estimation. In this work, we evaluate and analyze the impact of commonly used image similarity objectives in training DL registrations on raw tMRI. This is then compared with the Harmonic Phase-based approach, a traditional approach which is claimed to be robust to tag fading. Our findings, derived from both simulated images and an actual phantom scan, reveal the limitations of various similarity losses in raw tMRI and emphasize caution in registration tasks where image intensity changes over time.

Junyu Chen, Eric C. Frey, Yufan He et al.

In the last decade, convolutional neural networks (ConvNets) have been a major focus of research in medical image analysis. However, the performances of ConvNets may be limited by a lack of explicit consideration of the long-range spatial relationships in an image. Recently Vision Transformer architectures have been proposed to address the shortcomings of ConvNets and have produced state-of-the-art performances in many medical imaging applications. Transformers may be a strong candidate for image registration because their substantially larger receptive field enables a more precise comprehension of the spatial correspondence between moving and fixed images. Here, we present TransMorph, a hybrid Transformer-ConvNet model for volumetric medical image registration. This paper also presents diffeomorphic and Bayesian variants of TransMorph: the diffeomorphic variants ensure the topology-preserving deformations, and the Bayesian variant produces a well-calibrated registration uncertainty estimate. We extensively validated the proposed models using 3D medical images from three applications: inter-patient and atlas-to-patient brain MRI registration and phantom-to-CT registration. The proposed models are evaluated in comparison to a variety of existing registration methods and Transformer architectures. Qualitative and quantitative results demonstrate that the proposed Transformer-based model leads to a substantial performance improvement over the baseline methods, confirming the effectiveness of Transformers for medical image registration.

Junyu Chen, Evren Asma, Chung Chan

A convolutional neural network (ConvNet) is usually trained and then tested using images drawn from the same distribution. To generalize a ConvNet to various tasks often requires a complete training dataset that consists of images drawn from different tasks. In most scenarios, it is nearly impossible to collect every possible representative dataset as a priori. The new data may only become available after the ConvNet is deployed in clinical practice. ConvNet, however, may generate artifacts on out-of-distribution testing samples. In this study, we present Targeted Gradient Descent (TGD), a novel fine-tuning method that can extend a pre-trained network to a new task without revisiting data from the previous task while preserving the knowledge acquired from previous training. To a further extent, the proposed method also enables online learning of patient-specific data. The method is built on the idea of reusing a pre-trained ConvNet's redundant kernels to learn new knowledge. We compare the performance of TGD to several commonly used training approaches on the task of Positron emission tomography (PET) image denoising. Results from clinical images show that TGD generated results on par with training-from-scratch while significantly reducing data preparation and network training time. More importantly, it enables online learning on the testing study to enhance the network's generalization capability in real-world applications.

Junyu Chen, Yufan He, Eric C. Frey et al.

In the last decade, convolutional neural networks (ConvNets) have dominated and achieved state-of-the-art performances in a variety of medical imaging applications. However, the performances of ConvNets are still limited by lacking the understanding of long-range spatial relations in an image. The recently proposed Vision Transformer (ViT) for image classification uses a purely self-attention-based model that learns long-range spatial relations to focus on the relevant parts of an image. Nevertheless, ViT emphasizes the low-resolution features because of the consecutive downsamplings, result in a lack of detailed localization information, making it unsuitable for image registration. Recently, several ViT-based image segmentation methods have been combined with ConvNets to improve the recovery of detailed localization information. Inspired by them, we present ViT-V-Net, which bridges ViT and ConvNet to provide volumetric medical image registration. The experimental results presented here demonstrate that the proposed architecture achieves superior performance to several top-performing registration methods.

Junyu Chen, Eric C. Frey

For the majority of the learning-based segmentation methods, a large quantity of high-quality training data is required. In this paper, we present a novel learning-based segmentation model that could be trained semi- or un- supervised. Specifically, in the unsupervised setting, we parameterize the Active contour without edges (ACWE) framework via a convolutional neural network (ConvNet), and optimize the parameters of the ConvNet using a self-supervised method. In another setting (semi-supervised), the auxiliary segmentation ground truth is used during training. We show that the method provides fast and high-quality bone segmentation in the context of single-photon emission computed tomography (SPECT) image.