Yuanjing Feng

Jianzhong He, Fan Zhang, Yiang Pan et al.

The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body. Diffusion MRI tractography is the only method that enables the study of the anatomy and variability of the CST pathway in human health. In this work, we explored the performance of six widely used tractography methods for reconstructing the CST and its somatotopic organization. We perform experiments using diffusion MRI data from the Human Connectome Project. Four quantitative measurements including reconstruction rate, the WM-GM interface coverage, anatomical distribution of streamlines, and correlation with cortical volumes to assess the advantages and limitations of each method. Overall, we conclude that while current tractography methods have made progress toward the well-known challenge of improving the reconstruction of the lateral projections of the CST, the overall problem of performing a comprehensive CST reconstruction, including clinically important projections in the lateral (hand and face area) and medial portions (leg area), remains an important challenge for diffusion MRI tractography.

Sipei Li, Jianzhong He, Tengfei Xue et al.

The retinogeniculate pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time-consuming, has high clinical and expert labor costs, and affected by inter-observer variability. In this paper, we present what we believe is the first deep learning framework, namely DeepRGVP, to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure-informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a simple and successful streamline-level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non-RGVP streamlines. We perform comparisons with several state-of-the-art deep learning methods that were designed for tractography parcellation, and we show superior RGVP identification results using DeepRGVP.

Yuanjing Feng, Lei Xie, Jingqiang Wang et al.

Tractography traces the peak directions extracted from fiber orientation distribution (FOD) suffering from ambiguous spatial correspondences between diffusion directions and fiber geometry, which is prone to producing erroneous tracks while missing true positive connections. The peaks-based tractography methods 'locally' reconstructed streamlines in 'single to single' manner, thus lacking of global information about the trend of the whole fiber bundle. In this work, we propose a novel tractography method based on a bundle-specific tractogram distribution function by using a higher-order streamline differential equation, which reconstructs the streamline bundles in 'cluster to cluster' manner. A unified framework for any higher-order streamline differential equation is presented to describe the fiber bundles with disjoint streamlines defined based on the diffusion tensor vector field. At the global level, the tractography process is simplified as the estimation of bundle-specific tractogram distribution (BTD) coefficients by minimizing the energy optimization model, and is used to characterize the relations between BTD and diffusion tensor vector under the prior guidance by introducing the tractogram bundle information to provide anatomic priors. Experiments are performed on simulated Hough, Sine, Circle data, ISMRM 2015 Tractography Challenge data, FiberCup data, and in vivo data from the Human Connectome Project (HCP) data for qualitative and quantitative evaluation. The results demonstrate that our approach can reconstruct the complex global fiber bundles directly. BTD reduces the error deviation and accumulation at the local level and shows better results in reconstructing long-range, twisting, and large fanning tracts.

Alou Diakite, Cheng Li, Lei Xie et al.

Recent research has shown the potential of deep learning in multi-parametric MRI-based visual pathway (VP) segmentation. However, obtaining labeled data for training is laborious and time-consuming. Therefore, it is crucial to develop effective algorithms in situations with limited labeled samples. In this work, we propose a label-efficient deep learning method with self-ensembling (LESEN). LESEN incorporates supervised and unsupervised losses, enabling the student and teacher models to mutually learn from each other, forming a self-ensembling mean teacher framework. Additionally, we introduce a reliable unlabeled sample selection (RUSS) mechanism to further enhance LESEN's effectiveness. Our experiments on the human connectome project (HCP) dataset demonstrate the superior performance of our method when compared to state-of-the-art techniques, advancing multimodal VP segmentation for comprehensive analysis in clinical and research settings. The implementation code will be available at: https://github.com/aldiak/Semi-Supervised-Multimodal-Visual-Pathway- Delineation.

Lei Xie, Jiahao Huang, Jiawei Zhang et al.

Cranial nerves (CNs) play a crucial role in various essential functions of the human brain, and mapping their pathways from diffusion MRI (dMRI) provides valuable preoperative insights into the spatial relationships between individual CNs and key tissues. However, mapping a comprehensive and detailed CN atlas is challenging because of the unique anatomical structures of each CN pair and the complexity of the skull base environment.In this work, we present what we believe to be the first study to develop a comprehensive diffusion tractography atlas for automated mapping of CN pathways in the human brain. The CN atlas is generated by fiber clustering by using the streamlines generated by multi-parametric fiber tractography for each pair of CNs. Instead of disposable clustering, we explore a new strategy of multi-stage fiber clustering for multiple analysis of approximately 1,000,000 streamlines generated from the 50 subjects from the Human Connectome Project (HCP). Quantitative and visual experiments demonstrate that our CN atlas achieves high spatial correspondence with expert manual annotations on multiple acquisition sites, including the HCP dataset, the Multi-shell Diffusion MRI (MDM) dataset and two clinical cases of pituitary adenoma patients. The proposed CN atlas can automatically identify 8 fiber bundles associated with 5 pairs of CNs, including the optic nerve CN II, oculomotor nerve CN III, trigeminal nerve CN V and facial-vestibulocochlear nerve CN VII/VIII, and its robustness is demonstrated experimentally. This work contributes to the field of diffusion imaging by facilitating more efficient and automated mapping the pathways of multiple pairs of CNs, thereby enhancing the analysis and understanding of complex brain structures through visualization of their spatial relationships with nearby anatomy.

Lei Xie, Junxiong Huang, Yuanjing Feng et al.

The parcellation of Cranial Nerves (CNs) serves as a crucial quantitative methodology for evaluating the morphological characteristics and anatomical pathways of specific CNs. Multi-modal CNs parcellation networks have achieved promising segmentation performance, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI. However, insufficient exploration of diffusion MRI information has led to low performance of existing multi-modal fusion. In this work, we propose a tractography-guided Dual-label Collaborative Learning Network (DCLNet) for multi-modal CNs parcellation. The key contribution of our DCLNet is the introduction of coarse labels of CNs obtained from fiber tractography through CN atlas, and collaborative learning with precise labels annotated by experts. Meanwhile, we introduce a Modality-adaptive Encoder Module (MEM) to achieve soft information swapping between structural MRI and diffusion MRI. Extensive experiments conducted on the publicly available Human Connectome Project (HCP) dataset demonstrate performance improvements compared to single-label network. This systematic validation underscores the effectiveness of dual-label strategies in addressing inherent ambiguities in CNs parcellation tasks.

Lei Xie, Huajun Zhou, Junxiong Huang et al.

The segmentation of cranial nerves (CNs) tract provides a valuable quantitative tool for the analysis of the morphology and trajectory of individual CNs. Multimodal CNs tract segmentation networks, e.g., CNTSeg, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI, have achieved promising segmentation performance. However, it is laborious or even infeasible to collect complete multimodal data in clinical practice due to limitations in equipment, user privacy, and working conditions. In this work, we propose a novel arbitrary-modal fusion network for volumetric CNs tract segmentation, called CNTSeg-v2, which trains one model to handle different combinations of available modalities. Instead of directly combining all the modalities, we select T1-weighted (T1w) images as the primary modality due to its simplicity in data acquisition and contribution most to the results, which supervises the information selection of other auxiliary modalities. Our model encompasses an Arbitrary-Modal Collaboration Module (ACM) designed to effectively extract informative features from other auxiliary modalities, guided by the supervision of T1w images. Meanwhile, we construct a Deep Distance-guided Multi-stage (DDM) decoder to correct small errors and discontinuities through signed distance maps to improve segmentation accuracy. We evaluate our CNTSeg-v2 on the Human Connectome Project (HCP) dataset and the clinical Multi-shell Diffusion MRI (MDM) dataset. Extensive experimental results show that our CNTSeg-v2 achieves state-of-the-art segmentation performance, outperforming all competing methods.