Kai Xuan

Xin Wang, Sheng Wang, Honglin Xiong et al.

Magnetic resonance (MR) images collected in 2D clinical protocols typically have large inter-slice spacing, resulting in high in-plane resolution and reduced through-plane resolution. Super-resolution technique can enhance the through-plane resolution of MR images to facilitate downstream visualization and computer-aided diagnosis. However, most existing works train the super-resolution network at a fixed scaling factor, which is not friendly to clinical scenes of varying inter-slice spacing in MR scanning. Inspired by the recent progress in implicit neural representation, we propose a Spatial Attention-based Implicit Neural Representation (SA-INR) network for arbitrary reduction of MR inter-slice spacing. The SA-INR aims to represent an MR image as a continuous implicit function of 3D coordinates. In this way, the SA-INR can reconstruct the MR image with arbitrary inter-slice spacing by continuously sampling the coordinates in 3D space. In particular, a local-aware spatial attention operation is introduced to model nearby voxels and their affinity more accurately in a larger receptive field. Meanwhile, to improve the computational efficiency, a gradient-guided gating mask is proposed for applying the local-aware spatial attention to selected areas only. We evaluate our method on the public HCP-1200 dataset and the clinical knee MR dataset to demonstrate its superiority over other existing methods.

Xin Wang, Zhenrong Shen, Zhiyun Song et al.

Magnetic resonance (MR) images collected in 2D scanning protocols typically have large inter-slice spacing, resulting in high in-plane resolution but reduced through-plane resolution. Super-resolution techniques can reduce the inter-slice spacing of 2D scanned MR images, facilitating the downstream visual experience and computer-aided diagnosis. However, most existing super-resolution methods are trained at a fixed scaling ratio, which is inconvenient in clinical settings where MR scanning may have varying inter-slice spacings. To solve this issue, we propose Hierarchical Feature Conditional Diffusion (HiFi-Diff)} for arbitrary reduction of MR inter-slice spacing. Given two adjacent MR slices and the relative positional offset, HiFi-Diff can iteratively convert a Gaussian noise map into any desired in-between MR slice. Furthermore, to enable fine-grained conditioning, the Hierarchical Feature Extraction (HiFE) module is proposed to hierarchically extract conditional features and conduct element-wise modulation. Our experimental results on the publicly available HCP-1200 dataset demonstrate the high-fidelity super-resolution capability of HiFi-Diff and its efficacy in enhancing downstream segmentation performance.

Xiangyu Zhao, Di Zang, Sheng Wang et al.

Brain network analysis for traumatic brain injury (TBI) patients is critical for its consciousness level assessment and prognosis evaluation, which requires the segmentation of certain consciousness-related brain regions. However, it is difficult to construct a TBI segmentation model as manually annotated MR scans of TBI patients are hard to collect. Data augmentation techniques can be applied to alleviate the issue of data scarcity. However, conventional data augmentation strategies such as spatial and intensity transformation are unable to mimic the deformation and lesions in traumatic brains, which limits the performance of the subsequent segmentation task. To address these issues, we propose a novel medical image inpainting model named TBI-GAN to synthesize TBI MR scans with paired brain label maps. The main strength of our TBI-GAN method is that it can generate TBI images and corresponding label maps simultaneously, which has not been achieved in the previous inpainting methods for medical images. We first generate the inpainted image under the guidance of edge information following a coarse-to-fine manner, and then the synthesized intensity image is used as the prior for label inpainting. Furthermore, we introduce a registration-based template augmentation pipeline to increase the diversity of the synthesized image pairs and enhance the capacity of data augmentation. Experimental results show that the proposed TBI-GAN method can produce sufficient synthesized TBI images with high quality and valid label maps, which can greatly improve the 2D and 3D traumatic brain segmentation performance compared with the alternatives.

Jiangdong Cai, Yan Chen, Zhenrong Shen et al.

In digital pathology, acquiring all-in-focus images is essential to high-quality imaging and high-efficient clinical workflow. Traditional scanners achieve this by scanning at multiple focal planes of varying depths and then merging them, which is relatively slow and often struggles with complex tissue defocus. Recent prevailing image restoration technique provides a means to restore high-quality pathology images from scans of single focal planes. However, existing image restoration methods are inadequate, due to intricate defocus patterns in pathology images and their domain-specific semantic complexities. In this work, we devise a two-stage restoration solution cascading a transformer and a diffusion model, to benefit from their powers in preserving image fidelity and perceptual quality, respectively. We particularly propose a novel mixture of prompts for the two-stage solution. Given initial prompt that models defocus in microscopic imaging, we design two prompts that describe the high-level image semantics from pathology foundation model and the fine-grained tissue structures via edge extraction. We demonstrate that, by feeding the prompt mixture to our method, we can restore high-quality pathology images from single-focal-plane scans, implying high potentials of the mixture of prompts to clinical usage. Code will be publicly available at https://github.com/caijd2000/MoP.

Kai Xuan, Lei Xiang, Xiaoqian Huang et al.

In clinical practice, multi-modal magnetic resonance imaging (MRI) with different contrasts is usually acquired in a single study to assess different properties of the same region of interest in the human body. The whole acquisition process can be accelerated by having one or more modalities under-sampled in the $k$-space. Recent research has shown that, considering the redundancy between different modalities, a target MRI modality under-sampled in the $k$-space can be more efficiently reconstructed with a fully-sampled reference MRI modality. However, we find that the performance of the aforementioned multi-modal reconstruction can be negatively affected by subtle spatial misalignment between different modalities, which is actually common in clinical practice. In this paper, we improve the quality of multi-modal reconstruction by compensating for such spatial misalignment with a spatial alignment network. First, our spatial alignment network estimates the displacement between the fully-sampled reference and the under-sampled target images, and warps the reference image accordingly. Then, the aligned fully-sampled reference image joins the multi-modal reconstruction of the under-sampled target image. Also, considering the contrast difference between the target and reference images, we have designed a cross-modality-synthesis-based registration loss in combination with the reconstruction loss, to jointly train the spatial alignment network and the reconstruction network. The experiments on both clinical MRI and multi-coil $k$-space raw data demonstrate the superiority and robustness of the multi-modal MRI reconstruction empowered with our spatial alignment network. Our code is publicly available at \url{https://github.com/woxuankai/SpatialAlignmentNetwork}.

Zixu Zhuang, Liping Si, Sheng Wang et al.

Knee osteoarthritis (OA) is the most common osteoarthritis and a leading cause of disability. Cartilage defects are regarded as major manifestations of knee OA, which are visible by magnetic resonance imaging (MRI). Thus early detection and assessment for knee cartilage defects are important for protecting patients from knee OA. In this way, many attempts have been made on knee cartilage defect assessment by applying convolutional neural networks (CNNs) to knee MRI. However, the physiologic characteristics of the cartilage may hinder such efforts: the cartilage is a thin curved layer, implying that only a small portion of voxels in knee MRI can contribute to the cartilage defect assessment; heterogeneous scanning protocols further challenge the feasibility of the CNNs in clinical practice; the CNN-based knee cartilage evaluation results lack interpretability. To address these challenges, we model the cartilages structure and appearance from knee MRI into a graph representation, which is capable of handling highly diverse clinical data. Then, guided by the cartilage graph representation, we design a non-Euclidean deep learning network with the self-attention mechanism, to extract cartilage features in the local and global, and to derive the final assessment with a visualized result. Our comprehensive experiments show that the proposed method yields superior performance in knee cartilage defect assessment, plus its convenient 3D visualization for interpretability.

Zhiyuan Zhou, Kai Xuan, Zhifu Tao et al.

Due to the fact that basic uncertain information provides a simple form for decision information with certainty degree, it has been developed to reflect the quality of observed or subjective assessments. In order to study the algebra structure and preference relation of basic uncertain information, we develop some algebra operations for basic uncertain information. The order relation of such type of information has also been considered. Finally, to apply the developed algebra operations and order relations, a generalized TODIM method for multi-attribute decision making with basic uncertain information is given. The numerical example shows that the developed decision procedure is valid.

Jiayu Huo, Liping Si, Xi Ouyang et al.

Knee osteoarthritis (OA) is one of the most common musculoskeletal disorders and requires early-stage diagnosis. Nowadays, the deep convolutional neural networks have achieved greatly in the computer-aided diagnosis field. However, the construction of the deep learning models usually requires great amounts of annotated data, which is generally high-cost. In this paper, we propose a novel approach for knee cartilage defects assessment, including severity classification and lesion localization. This can be treated as a subtask of knee OA diagnosis. Particularly, we design a self-ensembling framework, which is composed of a student network and a teacher network with the same structure. The student network learns from both labeled data and unlabeled data and the teacher network averages the student model weights through the training course. A novel attention loss function is developed to obtain accurate attention masks. With dual-consistency checking of the attention in the lesion classification and localization, the two networks can gradually optimize the attention distribution and improve the performance of each other, whereas the training relies on partially labeled data only and follows the semi-supervised manner. Experiments show that the proposed method can significantly improve the self-ensembling performance in both knee cartilage defects classification and localization, and also greatly reduce the needs of annotated data.

Xuhua Ren, Jiayu Huo, Kai Xuan et al.

Brain magnetic resonance (MR) segmentation for hydrocephalus patients is considered as a challenging work. Encoding the variation of the brain anatomical structures from different individuals cannot be easily achieved. The task becomes even more difficult especially when the image data from hydrocephalus patients are considered, which often have large deformations and differ significantly from the normal subjects. Here, we propose a novel strategy with hard and soft attention modules to solve the segmentation problems for hydrocephalus MR images. Our main contributions are three-fold: 1) the hard-attention module generates coarse segmentation map using multi-atlas-based method and the VoxelMorph tool, which guides subsequent segmentation process and improves its robustness; 2) the soft-attention module incorporates position attention to capture precise context information, which further improves the segmentation accuracy; 3) we validate our method by segmenting insula, thalamus and many other regions-of-interests (ROIs) that are critical to quantify brain MR images of hydrocephalus patients in real clinical scenario. The proposed method achieves much improved robustness and accuracy when segmenting all 17 consciousness-related ROIs with high variations for different subjects. To the best of our knowledge, this is the first work to employ deep learning for solving the brain segmentation problems of hydrocephalus patients.