Constructing hierarchical attentive functional brain networks for early AD diagnosis.

Analyzing functional brain networks (FBN) with deep learning has demonstrated great potential for brain disorder diagnosis. The conventional construction of FBN is typically conducted at a single scale with a predefined brain region atlas. However, numerous studies have identified that the structure and function of the brain are hierarchically organized in nature. This urges the need of representing FBN in a hierarchical manner for more effective analysis of the complementary diagnostic insights at different scales. To this end, this paper proposes to build hierarchical FBNs adaptively within the Transformer framework. Specifically, a sparse attention-based node-merging module is designed to work alongside the conventional network feature extraction modules in each layer. The proposed module generates coarser nodes for further FBN construction and analysis by combining fine-grained nodes. By stacking multiple such layers, a hierarchical representation of FBN can be adaptively learned in an end-to-end manner. The hierarchical structure can not only integrate the complementary information from multiscale FBN for joint analysis, but also reduce the model complexity due to decreasing node sizes. Moreover, this paper argues that the nodes defined by the existing atlases are not necessarily the optimal starting level to build FBN hierarchy and exploring finer nodes may further enrich the FBN representation. In this regard, each predefined node in an atlas is split into multiple sub-nodes, overcoming the scale limitation of the existing atlases. Extensive experiments conducted on various data sets consistently demonstrate the superior performance of the proposed method over the competing methods.

ScribFormer: Transformer Makes CNN Work Better for Scribble-based Medical Image Segmentation.

Most recent scribble-supervised segmentation methods commonly adopt a CNN framework with an encoder-decoder architecture. Despite its multiple benefits, this framework generally can only capture small-range feature dependency for the convolutional layer with the local receptive field, which makes it difficult to learn global shape information from the limited information provided by scribble annotations. To address this issue, this paper proposes a new CNN-Transformer hybrid solution for scribble-supervised medical image segmentation called ScribFormer. The proposed ScribFormer model has a triple-branch structure, i.e., the hybrid of a CNN branch, a Transformer branch, and an attention-guided class activation map (ACAM) branch. Specifically, the CNN branch collaborates with the Transformer branch to fuse the local features learned from CNN with the global representations obtained from Transformer, which can effectively overcome limitations of existing scribble-supervised segmentation methods. Furthermore, the ACAM branch assists in unifying the shallow convolution features and the deep convolution features to improve model's performance further. Extensive experiments on two public datasets and one private dataset show that our ScribFormer has superior performance over the state-of-the-art scribble-supervised segmentation methods, and achieves even better results than the fully-supervised segmentation methods. The code is released at https://github.com/HUANGLIZI/ScribFormer.

Multimodal Brain Tumor Segmentation Boosted by Monomodal Normal Brain Images.

Many deep learning based methods have been proposed for brain tumor segmentation. Most studies focus on deep network internal structure to improve the segmentation accuracy, while valuable external information, such as normal brain appearance, is often ignored. Inspired by the fact that radiologists often screen lesion regions with normal appearance as reference in mind, in this paper, we propose a novel deep framework for brain tumor segmentation, where normal brain images are adopted as reference to compare with tumor brain images in a learned feature space. In this way, features at tumor regions, i.e., tumor-related features, can be highlighted and enhanced for accurate tumor segmentation. It is known that routine tumor brain images are multimodal, while normal brain images are often monomodal. This causes the feature comparison a big issue, i.e., multimodal vs. monomodal. To this end, we present a new feature alignment module (FAM) to make the feature distribution of monomodal normal brain images consistent/inconsistent with multimodal tumor brain images at normal/tumor regions, making the feature comparison effective. Both public (BraTS2022) and in-house tumor brain image datasets are used to evaluate our framework. Experimental results demonstrate that for both datasets, our framework can effectively improve the segmentation accuracy and outperforms the state-of-the-art segmentation methods. Codes are available at https://github.com/hb-liu/Normal-Brain-Boost-Tumor-Segmentation.

Multi-modal Modality-masked Diffusion Network for Brain MRI Synthesis with Random Modality Missing.

Synthesis of unavailable imaging modalities from available ones can generate modality-specific complementary information and enable multi-modality based medical images diagnosis or treatment. Existing generative methods for medical image synthesis are usually based on cross-modal translation between acquired and missing modalities. These methods are usually dedicated to specific missing modality and perform synthesis in one shot, which cannot deal with varying number of missing modalities flexibly and construct the mapping across modalities effectively. To address the above issues, in this paper, we propose a unified Multi-modal Modality-masked Diffusion Network (M2DN), tackling multi-modal synthesis from the perspective of "progressive whole-modality inpainting", instead of "cross-modal translation". Specifically, our M2DN considers the missing modalities as random noise and takes all the modalities as a unity in each reverse diffusion step. The proposed joint synthesis scheme performs synthesis for the missing modalities and self-reconstruction for the available ones, which not only enables synthesis for arbitrary missing scenarios, but also facilitates the construction of common latent space and enhances the model representation ability. Besides, we introduce a modality-mask scheme to encode availability status of each incoming modality explicitly in a binary mask, which is adopted as condition for the diffusion model to further enhance the synthesis performance of our M2DN for arbitrary missing scenarios. We carry out experiments on two public brain MRI datasets for synthesis and downstream segmentation tasks. Experimental results demonstrate that our M2DN outperforms the state-of-the-art models significantly and shows great generalizability for arbitrary missing modalities.

Dysfunctions of multiscale dynamic brain functional networks in subjective cognitive decline.

Subjective cognitive decline is potentially the earliest symptom of Alzheimer's disease, whose objective neurological basis remains elusive. To explore the potential biomarkers for subjective cognitive decline, we developed a novel deep learning method based on multiscale dynamical brain functional networks to identify subjective cognitive declines. We retrospectively constructed an internal data set (with 112 subjective cognitive decline and 64 healthy control subjects) to develop and internally validate the deep learning model. Conventional deep learning methods based on static and dynamic brain functional networks are compared. After the model is established, we prospectively collect an external data set (26 subjective cognitive decline and 12 healthy control subjects) for testing. Meanwhile, our method provides monitoring of the transitions between normal and abnormal (subjective cognitive decline-related) dynamical functional network states. The features of abnormal dynamical functional network states are quantified by network and variability metrics and associated with individual cognitions. Our method achieves an area under the receiver operating characteristic curve of 0.807 ± 0.046 in the internal validation data set and of 0.707 (P = 0.007) in the external testing data set, which shows improvements compared to conventional methods. The method further suggests that, at the local level, the abnormal dynamical functional network states are characterized by decreased connectivity strength and increased connectivity variability at different spatial scales. At the network level, the abnormal states are featured by scale-specifically altered modularity and all-scale decreased efficiency. Low tendencies to stay in abnormal states and high state transition variabilities are significantly associated with high general, language and executive functions. Overall, our work supports the deficits in multiscale brain dynamical functional networks detected by the deep learning method as reliable and meaningful neural alternation underpinning subjective cognitive decline.

One model, two brains: Automatic fetal brain extraction from MR images of twins.

Fetal brain extraction from magnetic resonance (MR) images is of great importance for both clinical applications and neuroscience studies. However, it is a challenging task, especially when dealing with twins, which are commonly existing in pregnancy. Currently, there is no brain extraction method dedicated to twins, raising significant demand to develop an effective twin fetal brain extraction method. To this end, we propose the first twin fetal brain extraction framework, which possesses three novel features. First, to narrow down the region of interest and preserve structural information between the two brains in twin fetal MR images, we take advantage of an advanced object detector to locate all the brains in twin fetal MR images at once. Second, we propose a Twin Fetal Brain Extraction Network (TFBE-Net) to further suppress insignificant features for segmenting brain regions. Finally, we propose a Two-step Training Strategy (TTS) to learn correlation features of the single fetal brain for further improving the performance of TFBE-Net. We validate the proposed framework on a twin fetal brain dataset. The experiments show that our framework achieves promising performance on both quantitative and qualitative evaluations, and outperforms state-of-the-art methods for fetal brain extraction.

Modality-Specific Information Disentanglement from Multi-parametric MRI for Breast Tumor Segmentation and Computer-aided Diagnosis.

Breast cancer is becoming a significant global health challenge, with millions of fatalities annually. Magnetic Resonance Imaging (MRI) can provide various sequences for characterizing tumor morphology and internal patterns, and becomes an effective tool for detection and diagnosis of breast tumors. However, previous deep-learning based tumor segmentation methods from multi-parametric MRI still have limitations in exploring inter-modality information and focusing task-informative modality/modalities. To address these shortcomings, we propose a Modality-Specific Information Disentanglement (MoSID) framework to extract both inter- and intra-modality attention maps as prior knowledge for guiding tumor segmentation. Specifically, by disentangling modality-specific information, the MoSID framework provides complementary clues for the segmentation task, by generating modality-specific attention maps to guide modality selection and inter-modality evaluation. Our experiments on two 3D breast datasets and one 2D prostate dataset demonstrate that the MoSID framework outperforms other state-of-the-art multi-modality segmentation methods, even in the cases of missing modalities. Based on the segmented lesions, we further train a classifier to predict the patients' response to radiotherapy. The prediction accuracy is comparable to the case of using manually-segmented tumors for treatment outcome prediction, indicating the robustness and effectiveness of the proposed segmentation method. The code is available at https://github.com/Qianqian-Chen/MoSID.

A Unified Multi-Modality Fusion Framework for Deep Spatio-Temporal-Spectral Feature Learning in Resting-State fMRI Denoising.

Resting-state functional magnetic resonance imaging (rs-fMRI) is a commonly used functional neuroimaging technique to investigate the functional brain networks. However, rs-fMRI data are often contaminated with noise and artifacts that adversely affect the results of rs-fMRI studies. Several machine/deep learning methods have achieved impressive performance to automatically regress the noise-related components decomposed from rs-fMRI data, which are expressed as the pairs of a spatial map and its associated time series. However, most of the previous methods individually analyze each modality of the noise-related components and simply aggregate the decision-level information (or knowledge) extracted from each modality to make a final decision. Moreover, these approaches consider only the limited modalities making it difficult to explore class-discriminative spectral information of noise-related components. To overcome these limitations, we propose a unified deep attentive spatio-spectral-temporal feature fusion framework. We first adopt a learnable wavelet transform module at the input-level of the framework to elaborately explore the spectral information in subsequent processes. We then construct a feature-level multi-modality fusion module to efficiently exchange the information from multi-modality inputs in the feature space. Finally, we design confidence-based voting strategies for decision-level fusion at the end of the framework to make a robust final decision. In our experiments, the proposed method achieved remarkable performance for noise-related component detection on various rs-fMRI datasets.

A deep learning system for predicting time to progression of diabetic retinopathy.

Diabetic retinopathy (DR) is the leading cause of preventable blindness worldwide. The risk of DR progression is highly variable among different individuals, making it difficult to predict risk and personalize screening intervals. We developed and validated a deep learning system (DeepDR Plus) to predict time to DR progression within 5 years solely from fundus images. First, we used 717,308 fundus images from 179,327 participants with diabetes to pretrain the system. Subsequently, we trained and validated the system with a multiethnic dataset comprising 118,868 images from 29,868 participants with diabetes. For predicting time to DR progression, the system achieved concordance indexes of 0.754-0.846 and integrated Brier scores of 0.153-0.241 for all times up to 5 years. Furthermore, we validated the system in real-world cohorts of participants with diabetes. The integration with clinical workflow could potentially extend the mean screening interval from 12 months to 31.97 months, and the percentage of participants recommended to be screened at 1-5 years was 30.62%, 20.00%, 19.63%, 11.85% and 17.89%, respectively, while delayed detection of progression to vision-threatening DR was 0.18%. Altogether, the DeepDR Plus system could predict individualized risk and time to DR progression over 5 years, potentially allowing personalized screening intervals.

DSMT-Net: Dual Self-Supervised Multi-Operator Transformation for Multi-Source Endoscopic Ultrasound Diagnosis.

Pancreatic cancer has the worst prognosis of all cancers. The clinical application of endoscopic ultrasound (EUS) for the assessment of pancreatic cancer risk and of deep learning for the classification of EUS images have been hindered by inter-grader variability and labeling capability. One of the key reasons for these difficulties is that EUS images are obtained from multiple sources with varying resolutions, effective regions, and interference signals, making the distribution of the data highly variable and negatively impacting the performance of deep learning models. Additionally, manual labeling of images is time-consuming and requires significant effort, leading to the desire to effectively utilize a large amount of unlabeled data for network training. To address these challenges, this study proposes the Dual Self-supervised Multi-Operator Transformation Network (DSMT-Net) for multi-source EUS diagnosis. The DSMT-Net includes a multi-operator transformation approach to standardize the extraction of regions of interest in EUS images and eliminate irrelevant pixels. Furthermore, a transformer-based dual self-supervised network is designed to integrate unlabeled EUS images for pre-training the representation model, which can be transferred to supervised tasks such as classification, detection, and segmentation. A large-scale EUS-based pancreas image dataset (LEPset) has been collected, including 3,500 pathologically proven labeled EUS images (from pancreatic and non-pancreatic cancers) and 8,000 unlabeled EUS images for model development. The self-supervised method has also been applied to breast cancer diagnosis and was compared to state-of-the-art deep learning models on both datasets. The results demonstrate that the DSMT-Net significantly improves the accuracy of pancreatic and breast cancer diagnosis.

An Anatomy- and Topology-Preserving Framework for Coronary Artery Segmentation.

Coronary artery segmentation is critical for coronary artery disease diagnosis but challenging due to its tortuous course with numerous small branches and inter-subject variations. Most existing studies ignore important anatomical information and vascular topologies, leading to less desirable segmentation performance that usually cannot satisfy clinical demands. To deal with these challenges, in this paper we propose an anatomy- and topology-preserving two-stage framework for coronary artery segmentation. The proposed framework consists of an anatomical dependency encoding (ADE) module and a hierarchical topology learning (HTL) module for coarse-to-fine segmentation, respectively. Specifically, the ADE module segments four heart chambers and aorta, and thus five distance field maps are obtained to encode distance between chamber surfaces and coarsely segmented coronary artery. Meanwhile, ADE also performs coronary artery detection to crop region-of-interest and eliminate foreground-background imbalance. The follow-up HTL module performs fine segmentation by exploiting three hierarchical vascular topologies, i.e., key points, centerlines, and neighbor connectivity using a multi-task learning scheme. In addition, we adopt a bottom-up attention interaction (BAI) module to integrate the feature representations extracted across hierarchical topologies. Extensive experiments on public and in-house datasets show that the proposed framework achieves state-of-the-art performance for coronary artery segmentation.

Image Recovery Matters: A Recovery-Extraction Framework for Robust Fetal Brain Extraction From MR Images.

The extraction of the fetal brain from magnetic resonance (MR) images is a challenging task. In particular, fetal MR images suffer from different kinds of artifacts introduced during the image acquisition. Among those artifacts, intensity inhomogeneity is a common one affecting brain extraction. In this work, we propose a deep learning-based recovery-extraction framework for fetal brain extraction, which is particularly effective in handling fetal MR images with intensity inhomogeneity. Our framework involves two stages. First, the artifact-corrupted images are recovered with the proposed generative adversarial learning-based image recovery network with a novel region-of-darkness discriminator that enforces the network focusing on artifacts of the images. Second, we propose a brain extraction network for more effective fetal brain segmentation by strengthening the association between lower- and higher-level features as well as suppressing task-irrelevant features. Thanks to the proposed recovery-extraction strategy, our framework is able to accurately segment fetal brains from artifact-corrupted MR images. The experiments show that our framework achieves promising performance in both quantitative and qualitative evaluations, and outperforms state-of-the-art methods in both image recovery and fetal brain extraction.

Deep learning-assisted preclinical MR fingerprinting for sub-millimeter T1 and T2 mapping of entire macaque brain.

PURPOSE: Preclinical MR fingerprinting (MRF) suffers from long acquisition time for organ-level coverage due to demanding image resolution and limited undersampling capacity. This study aims to develop a deep learning-assisted fast MRF framework for sub-millimeter T1 and T2 mapping of entire macaque brain on a preclinical 9.4 T MR system. METHODS: Three dimensional MRF images were reconstructed by singular value decomposition (SVD) compressed reconstruction. T1 and T2 mapping for each axial slice exploited a self-attention assisted residual U-Net to suppress aliasing-induced quantification errors, and the transmit-field (B1 + ) measurements for robustness against B1 + inhomogeneity. Supervised network training used MRF images simulated via virtual parametric maps and a desired undersampling scheme. This strategy bypassed the difficulties of acquiring fully sampled preclinical MRF data to guide network training. The proposed fast MRF framework was tested on experimental data acquired from ex vivo and in vivo macaque brains. RESULTS: The trained network showed reasonable adaptability to experimental MRF images, enabling robust delineation of various T1 and T2 distributions in the brain tissues. Further, the proposed MRF framework outperformed several existing fast MRF methods in handling the aliasing artifacts and capturing detailed cerebral structures in the mapping results. Parametric mapping of entire macaque brain at nominal resolution of 0.35 × $$ \times $$ 0.35 × $$ \times $$ 1 mm3 can be realized via a 20-min 3D MRF scan, which was sixfold faster than the baseline protocol. CONCLUSION: Introducing deep learning to MRF framework paves the way for efficient organ-level high-resolution quantitative MRI in preclinical applications.

A Novel Approach Analysing the Dynamic Brain Functional Connectivity for Improved MCI Detection.

OBJECTIVE: Dynamic functional connectivity (dFC) of the brain has been explored for the detection of mild cognitive impairment (MCI), preventing potential development of Alzheimer's disease. Deep learning is widely used method for dFC analysis but is unfortunately computationally expensive and unexplainable. Root mean square value (RMS) of the pairwise Pearson's correlation of the dFC is also proposed but is insufficient for accurate MCI detection. The present study aims at exploring the feasibility of several novel features for dFC analysis, and thus, reliable MCI detection. METHODS: A public resting-state functional magnetic resonance imaging dataset containing healthy controls (HC), early MCI (eMCI), and late MCI (lMCI) patients was used. In addition to RMS, nine features were extracted from the pairwise Pearson's correlation of the dFC, inducing amplitude-, spectral-, entropy-, and autocorrelation-related features, and time reversibility. A Student's t-test and a least absolute shrinkage and selection operator (LASSO) regression were employed for feature dimension reduction. A SVM was then adopted for two classification objectives: HC vs. lMCI and HC vs. eMCI. Accuracy, sensitivity, specificity, F1-score, and area under the receiver operating characteristic curve were calculated as performance metrics. RESULTS: 6109 out of 66700 features are significantly different between HC and lMCI and 5905 between HC and eMCI. Besides, the proposed features produce excellent classification results for both tasks, outperforming most of the existing methods. SIGNIFICANCE: This study proposes a novel and general framework for dFC analysis, providing a promising tool for the detection of many neurological brain diseases using different brain signals.

DTR-Net: Dual-Space 3D Tooth Model Reconstruction From Panoramic X-Ray Images.

In digital dentistry, cone-beam computed tomography (CBCT) can provide complete 3D tooth models, yet suffers from a long concern of requiring excessive radiation dose and higher expense. Therefore, 3D tooth model reconstruction from 2D panoramic X-ray image is more cost-effective, and has attracted great interest in clinical applications. In this paper, we propose a novel dual-space framework, namely DTR-Net, to reconstruct 3D tooth model from 2D panoramic X-ray images in both image and geometric spaces. Specifically, in the image space, we apply a 2D-to-3D generative model to recover intensities of CBCT image, guided by a task-oriented tooth segmentation network in a collaborative training manner. Meanwhile, in the geometric space, we benefit from an implicit function network in the continuous space, learning using points to capture complicated tooth shapes with geometric properties. Experimental results demonstrate that our proposed DTR-Net achieves state-of-the-art performance both quantitatively and qualitatively in 3D tooth model reconstruction, indicating its potential application in dental practice.

Joint Cross-Attention Network With Deep Modality Prior for Fast MRI Reconstruction.

Current deep learning-based reconstruction models for accelerated multi-coil magnetic resonance imaging (MRI) mainly focus on subsampled k-space data of single modality using convolutional neural network (CNN). Although dual-domain information and data consistency constraint are commonly adopted in fast MRI reconstruction, the performance of existing models is still limited mainly by three factors: inaccurate estimation of coil sensitivity, inadequate utilization of structural prior, and inductive bias of CNN. To tackle these challenges, we propose an unrolling-based joint Cross-Attention Network, dubbed as jCAN, using deep guidance of the already acquired intra-subject data. Particularly, to improve the performance of coil sensitivity estimation, we simultaneously optimize the latent MR image and sensitivity map (SM). Besides, we introduce Gating layer and Gaussian layer into SM estimation to alleviate the "defocus" and "over-coupling" effects and further ameliorate the SM estimation. To enhance the representation ability of the proposed model, we deploy Vision Transformer (ViT) and CNN in the image and k-space domains, respectively. Moreover, we exploit pre-acquired intra-subject scan as reference modality to guide the reconstruction of subsampled target modality by resorting to the self- and cross-attention scheme. Experimental results on public knee and in-house brain datasets demonstrate that the proposed jCAN outperforms the state-of-the-art methods by a large margin in terms of SSIM and PSNR for different acceleration factors and sampling masks. Our code is publicly available at https://github.com/sunkg/jCAN.

Beam-wise dose composition learning for head and neck cancer dose prediction in radiotherapy.

Automatic and accurate dose distribution prediction plays an important role in radiotherapy plan. Although previous methods can provide promising performance, most methods did not consider beam-shaped radiation of treatment delivery in clinical practice. This leads to inaccurate prediction, especially on beam paths. To solve this problem, we propose a beam-wise dose composition learning (BDCL) method for dose prediction in the context of head and neck (H&N) radiotherapy plan. Specifically, a global dose network is first utilized to predict coarse dose values in the whole-image space. Then, we propose to generate individual beam masks to decompose the coarse dose distribution into multiple field doses, called beam voters, which are further refined by a subsequent beam dose network and reassembled to form the final dose distribution. In particular, we design an overlap consistency module to keep the similarity of high-level features in overlapping regions between different beam voters. To make the predicted dose distribution more consistent with the real radiotherapy plan, we also propose a dose-volume histogram (DVH) calibration process to facilitate feature learning in some clinically concerned regions. We further apply an edge enhancement procedure to enhance the learning of the extracted feature from the dose falloff regions. Experimental results on a public H&N cancer dataset from the AAPM OpenKBP challenge show that our method achieves superior performance over other state-of-the-art approaches by significant margins. Source code is released at https://github.com/TL9792/BDCLDosePrediction.

A progressive framework for tooth and substructure segmentation from cone-beam CT images.

BACKGROUND: Accurate segmentation of individual tooth and their substructures including enamel, pulp, and dentin from cone-beam computed tomography (CBCT) images is essential for dental diagnosis and treatment planning in digital dentistry. Existing methods for tooth segmentation based on CBCT images have achieved substantial progress; however, techniques for further segmentation into substructures are yet to be developed. PURPOSE: We aim to propose a novel three-stage progressive deep-learning-based framework for automatically segmenting 3D tooth from CBCT images, focusing on finer substructures, i.e., enamel, pulp, and dentin. METHODS: In this paper, we first detect each tooth using its centroid by a clustering scheme, which efficiently determines each tooth detection by applying learned displacement vectors from the foreground tooth region. Next, guided by the detected centroid, each tooth proposal, combined with the corresponding tooth map, is processed through our tooth segmentation network. We also present an attention-based hybrid feature fusion mechanism, which provides intricate details of the tooth boundary while maintaining the global tooth shape, thereby enhancing the segmentation process. Additionally, we utilize the skeleton of the tooth as a guide for subsequent substructure segmentation. RESULTS: Our algorithm is extensively evaluated on a collected dataset of 314 patients, and the extensive comparison and ablation studies demonstrate superior segmentation results of our approach. CONCLUSIONS: Our proposed method can automatically segment tooth and finer substructures from CBCT images, underlining its potential applicability for clinical diagnosis and surgical treatment.

Coarse-to-fine registration and time-intensity curves constraint for liver DCE-MRI synthesis.

Image registration plays a crucial role in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), used as a fundamental step for the subsequent diagnosis of benign and malignant tumors. However, the registration process encounters significant challenges due to the substantial intensity changes observed among different time points, resulting from the injection of contrast agents. Furthermore, previous studies have often overlooked the alignment of small structures, such as tumors and vessels. In this work, we propose a novel DCE-MRI registration framework that can effectively align the DCE-MRI time series. Specifically, our DCE-MRI registration framework consists of two steps, i.e., a de-enhancement synthesis step and a coarse-to-fine registration step. In the de-enhancement synthesis step, a disentanglement network separates DCE-MRI images into a content component representing the anatomical structures and a style component indicating the presence or absence of contrast agents. This step generates synthetic images where the contrast agents are removed from the original images, alleviating the negative effects of intensity changes on the subsequent registration process. In the registration step, we utilize a coarse registration network followed by a refined registration network. These two networks facilitate the estimation of both the coarse and refined displacement vector fields (DVFs) in a pairwise and groupwise registration manner, respectively. In addition, to enhance the alignment accuracy for small structures, a voxel-wise constraint is further conducted by assessing the smoothness of the time-intensity curves (TICs). Experimental results on liver DCE-MRI demonstrate that our proposed method outperforms state-of-the-art approaches, offering more robust and accurate alignment results.

3D multi-modality Transformer-GAN for high-quality PET reconstruction.

Positron emission tomography (PET) scans can reveal abnormal metabolic activities of cells and provide favorable information for clinical patient diagnosis. Generally, standard-dose PET (SPET) images contain more diagnostic information than low-dose PET (LPET) images but higher-dose scans can also bring higher potential radiation risks. To reduce the radiation risk while acquiring high-quality PET images, in this paper, we propose a 3D multi-modality edge-aware Transformer-GAN for high-quality SPET reconstruction using the corresponding LPET images and T1 acquisitions from magnetic resonance imaging (T1-MRI). Specifically, to fully excavate the metabolic distributions in LPET and anatomical structural information in T1-MRI, we first use two separate CNN-based encoders to extract local spatial features from the two modalities, respectively, and design a multimodal feature integration module to effectively integrate the two kinds of features given the diverse contributions of features at different locations. Then, as CNNs can describe local spatial information well but have difficulty in modeling long-range dependencies in images, we further apply a Transformer-based encoder to extract global semantic information in the input images and use a CNN decoder to transform the encoded features into SPET images. Finally, a patch-based discriminator is applied to ensure the similarity of patch-wise data distribution between the reconstructed and real images. Considering the importance of edge information in anatomical structures for clinical disease diagnosis, besides voxel-level estimation error and adversarial loss, we also introduce an edge-aware loss to retain more edge detail information in the reconstructed SPET images. Experiments on the phantom dataset and clinical dataset validate that our proposed method can effectively reconstruct high-quality SPET images and outperform current state-of-the-art methods in terms of qualitative and quantitative metrics.