In this study, we developed an Evidence-based Ensemble Neural Network, namely EVENet, for anatomical brain parcellation using diffusion MRI. The key innovation of EVENet is the design of an evidential deep learning framework to quantify predictive uncertainty at each voxel during a single inference. To do so, we design an evidence-based ensemble learning framework for uncertainty-aware parcellation to leverage the multiple dMRI parameters derived from diffusion MRI. Using EVENet, we obtained accurate parcellation and uncertainty estimates across different datasets from healthy and clinical populations and with different imaging acquisitions. The overall network includes five parallel subnetworks, where each is dedicated to learning the FreeSurfer parcellation for a certain diffusion MRI parameter. An evidence-based ensemble methodology is then proposed to fuse the individual outputs. We perform experimental evaluations on large-scale datasets from multiple imaging sources, including high-quality diffusion MRI data from healthy adults and clinically diffusion MRI data from participants with various brain diseases (schizophrenia, bipolar disorder, attention-deficit/hyperactivity disorder, Parkinson's disease, cerebral small vessel disease, and neurosurgical patients with brain tumors). Compared to several state-of-the-art methods, our experimental results demonstrate highly improved parcellation accuracy across the multiple testing datasets despite the differences in dMRI acquisition protocols and health conditions. Furthermore, thanks to the uncertainty estimation, our EVENet approach demonstrates a good ability to detect abnormal brain regions in patients with lesions, enhancing the interpretability and reliability of the segmentation results.
Image denoising is a critical component in a camera's Image Signal Processing (ISP) pipeline. There are two typical ways to inject a denoiser into the ISP pipeline: applying a denoiser directly to captured raw frames (raw domain) or to the ISP's output sRGB images (sRGB domain). However, both approaches have their limitations. Residual noise from raw-domain denoising can be amplified by the subsequent ISP processing, and the sRGB domain struggles to handle spatially varying noise since it only sees noise distorted by the ISP. Consequently, most raw or sRGB domain denoising works only for specific noise distributions and ISP configurations. To address these challenges, we propose DualDn, a novel learning-based dual-domain denoising. Unlike previous single-domain denoising, DualDn consists of two denoising networks: one in the raw domain and one in the sRGB domain. The raw domain denoising adapts to sensor-specific noise as well as spatially varying noise levels, while the sRGB domain denoising adapts to ISP variations and removes residual noise amplified by the ISP. Both denoising networks are connected with a differentiable ISP, which is trained end-to-end and discarded during the inference stage. With this design, DualDn achieves greater generalizability compared to most learning-based denoising methods, as it can adapt to different unseen noises, ISP parameters, and even novel ISP pipelines. Experiments show that DualDn achieves state-of-the-art performance and can adapt to different denoising architectures. Moreover, DualDn can be used as a plug-and-play denoising module with real cameras without retraining, and still demonstrate better performance than commercial on-camera denoising. The project website is available at: https://openimaginglab.github.io/DualDn/
Brain imaging studies have demonstrated that diffusion MRI tractography geometric shape descriptors can inform the study of the brain's white matter pathways and their relationship to brain function. In this work, we investigate the possibility of utilizing a deep learning model to compute shape measures of the brain's white matter connections. We introduce a novel framework, TractShapeNet, that leverages a point cloud representation of tractography to compute five shape measures: length, span, volume, total surface area, and irregularity. We assess the performance of the method on a large dataset including 1065 healthy young adults. Experiments for shape measure computation demonstrate that our proposed TractShapeNet outperforms other point cloud-based neural network models in both the Pearson correlation coefficient and normalized error metrics. We compare the inference runtime results with the conventional shape computation tool DSI-Studio. Our results demonstrate that a deep learning approach enables faster and more efficient shape measure computation. We also conduct experiments on two downstream language cognition prediction tasks, showing that shape measures from TractShapeNet perform similarly to those computed by DSI-Studio. Our code will be available at: https://github.com/SlicerDMRI/TractShapeNet.
Speech-driven gesture generation is an emerging domain within virtual human creation, where current methods predominantly utilize Transformer-based architectures that necessitate extensive memory and are characterized by slow inference speeds. In response to these limitations, we propose \textit{DiM-Gestures}, a novel end-to-end generative model crafted to create highly personalized 3D full-body gestures solely from raw speech audio, employing Mamba-based architectures. This model integrates a Mamba-based fuzzy feature extractor with a non-autoregressive Adaptive Layer Normalization (AdaLN) Mamba-2 diffusion architecture. The extractor, leveraging a Mamba framework and a WavLM pre-trained model, autonomously derives implicit, continuous fuzzy features, which are then unified into a singular latent feature. This feature is processed by the AdaLN Mamba-2, which implements a uniform conditional mechanism across all tokens to robustly model the interplay between the fuzzy features and the resultant gesture sequence. This innovative approach guarantees high fidelity in gesture-speech synchronization while maintaining the naturalness of the gestures. Employing a diffusion model for training and inference, our framework has undergone extensive subjective and objective evaluations on the ZEGGS and BEAT datasets. These assessments substantiate our model's enhanced performance relative to contemporary state-of-the-art methods, demonstrating competitive outcomes with the DiTs architecture (Persona-Gestors) while optimizing memory usage and accelerating inference speed.
Diffusion magnetic resonance imaging (dMRI) provides critical insights into the microstructural and connectional organization of the human brain. However, the availability of high-field, open-access datasets that include raw k-space data for advanced research remains limited. To address this gap, we introduce Diff5T, a first comprehensive 5.0 Tesla diffusion MRI dataset focusing on the human brain. This dataset includes raw k-space data and reconstructed diffusion images, acquired using a variety of imaging protocols. Diff5T is designed to support the development and benchmarking of innovative methods in artifact correction, image reconstruction, image preprocessing, diffusion modelling and tractography. The dataset features a wide range of diffusion parameters, including multiple b-values and gradient directions, allowing extensive research applications in studying human brain microstructure and connectivity. With its emphasis on open accessibility and detailed benchmarks, Diff5T serves as a valuable resource for advancing human brain mapping research using diffusion MRI, fostering reproducibility, and enabling collaboration across the neuroscience and medical imaging communities.
Tractography fiber clustering using diffusion MRI (dMRI) is a crucial strategy for white matter (WM) parcellation. Current methods primarily use the geometric information of fibers (i.e., the spatial trajectories) to group similar fibers into clusters, overlooking the important functional signals present along the fiber tracts. There is increasing evidence that neural activity in the WM can be measured using functional MRI (fMRI), offering potentially valuable multimodal information for fiber clustering. In this paper, we develop a novel deep learning fiber clustering framework, namely Deep Multi-view Fiber Clustering (DMVFC), that uses joint dMRI and fMRI data to enable functionally consistent WM parcellation. DMVFC can effectively integrate the geometric characteristics of the WM fibers with the fMRI BOLD signals along the fiber tracts. It includes two major components: 1) a multi-view pretraining module to compute embedding features from fiber geometric information and functional signals separately, and 2) a collaborative fine-tuning module to simultaneously refine the two kinds of embeddings. In the experiments, we compare DMVFC with two state-of-the-art fiber clustering methods and demonstrate superior performance in achieving functionally meaningful and consistent WM parcellation results.
Nancy R. Newlin, Kurt Schilling, Serge Koudoro et al.
White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.
Registration of diffusion MRI tractography is an essential step for analyzing group similarities and variations in the brain's white matter (WM). Streamline-based registration approaches can leverage the 3D geometric information of fiber pathways to enable spatial alignment after registration. Existing methods usually rely on the optimization of the spatial distances to identify the optimal transformation. However, such methods overlook point connectivity patterns within the streamline itself, limiting their ability to identify anatomical correspondences across tractography datasets. In this work, we propose a novel unsupervised approach using deep learning to perform streamline-based dMRI tractography registration. The overall idea is to identify corresponding keypoint pairs across subjects for spatial alignment of tractography datasets. We model tractography as point clouds to leverage the graph connectivity along streamlines. We propose a novel keypoint detection method for streamlines, framed as a probabilistic classification task to identify anatomically consistent correspondences across unstructured streamline sets. In the experiments, we compare several existing methods and show highly effective and efficient tractography registration performance.
With the rapid development of gravitational wave astronomy, the increasing number of detected events necessitates efficient methods for parameter estimation and model updates. This study presents a novel approach using knowledge distillation techniques to enhance computational efficiency in gravitational wave analysis. We develop a framework combining ResNet1D and Inverse Autoregressive Flow (IAF) architectures, where knowledge from a complex teacher model is transferred to a lighter student model. Our experimental results show that the student model achieves a validation loss of 3.70 with optimal configuration (40,100,0.75), compared to the teacher model's 4.09, while reducing the number of parameters by 43\%. The Jensen-Shannon divergence between teacher and student models remains below 0.0001 across network layers, indicating successful knowledge transfer. By optimizing ResNet layers (7-16) and hidden features (70-120), we achieve a 35\% reduction in inference time while maintaining parameter estimation accuracy. This work demonstrates significant improvements in computational efficiency for gravitational wave data analysis, providing valuable insights for real-time event processing.
Speech-driven gesture generation using transformer-based generative models represents a rapidly advancing area within virtual human creation. However, existing models face significant challenges due to their quadratic time and space complexities, limiting scalability and efficiency. To address these limitations, we introduce DiM-Gestor, an innovative end-to-end generative model leveraging the Mamba-2 architecture. DiM-Gestor features a dual-component framework: (1) a fuzzy feature extractor and (2) a speech-to-gesture mapping module, both built on the Mamba-2. The fuzzy feature extractor, integrated with a Chinese Pre-trained Model and Mamba-2, autonomously extracts implicit, continuous speech features. These features are synthesized into a unified latent representation and then processed by the speech-to-gesture mapping module. This module employs an Adaptive Layer Normalization (AdaLN)-enhanced Mamba-2 mechanism to uniformly apply transformations across all sequence tokens. This enables precise modeling of the nuanced interplay between speech features and gesture dynamics. We utilize a diffusion model to train and infer diverse gesture outputs. Extensive subjective and objective evaluations conducted on the newly released Chinese Co-Speech Gestures dataset corroborate the efficacy of our proposed model. Compared with Transformer-based architecture, the assessments reveal that our approach delivers competitive results and significantly reduces memory usage, approximately 2.4 times, and enhances inference speeds by 2 to 4 times. Additionally, we released the CCG dataset, a Chinese Co-Speech Gestures dataset, comprising 15.97 hours (six styles across five scenarios) of 3D full-body skeleton gesture motion performed by professional Chinese TV broadcasters.
Medical image segmentation poses challenges due to domain gaps, data modality variations, and dependency on domain knowledge or experts, especially for low- and middle-income countries (LMICs). Whereas for humans, given a few exemplars (with corresponding labels), we are able to segment different medical images even without exten-sive domain-specific clinical training. In addition, current SAM-based medical segmentation models use fine-grained visual prompts, such as the bounding rectangle generated from manually annotated target segmentation mask, as the bounding box (bbox) prompt during the testing phase. However, in actual clinical scenarios, no such precise prior knowledge is available. Our experimental results also reveal that previous models nearly fail to predict when given coarser bbox prompts. Considering these issues, in this paper, we introduce a domain-aware selective adaptation approach to adapt the general knowledge learned from a large model trained with natural images to the corresponding medical domains/modalities, with access to only a few (e.g. less than 5) exemplars. Our method mitigates the aforementioned limitations, providing an efficient and LMICs-friendly solution. Extensive experimental analysis showcases the effectiveness of our approach, offering potential advancements in healthcare diagnostics and clinical applications in LMICs.