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.
Diffusion tensor imaging (DTI) holds significant importance in clinical diagnosis and neuroscience research. However, conventional model-based fitting methods often suffer from sensitivity to noise, leading to decreased accuracy in estimating DTI parameters. While traditional data-driven deep learning methods have shown potential in terms of accuracy and efficiency, their limited generalization to out-of-training-distribution data impedes their broader application due to the diverse scan protocols used across centers, scanners, and studies. This work aims to tackle these challenges and promote the use of DTI by introducing a data-driven optimization-based method termed DoDTI. DoDTI combines the weighted linear least squares fitting algorithm and regularization by denoising technique. The former fits DW images from diverse acquisition settings into diffusion tensor field, while the latter applies a deep learning-based denoiser to regularize the diffusion tensor field instead of the DW images, which is free from the limitation of fixed-channel assignment of the network. The optimization object is solved using the alternating direction method of multipliers and then unrolled to construct a deep neural network, leveraging a data-driven strategy to learn network parameters. Extensive validation experiments are conducted utilizing both internally simulated datasets and externally obtained in-vivo datasets. The results, encompassing both qualitative and quantitative analyses, showcase that the proposed method attains state-of-the-art performance in DTI parameter estimation. Notably, it demonstrates superior generalization, accuracy, and efficiency, rendering it highly reliable for widespread application in the field.
Diffusion MRI tractography technique enables non-invasive visualization of the white matter pathways in the brain. It plays a crucial role in neuroscience and clinical fields by facilitating the study of brain connectivity and neurological disorders. However, the accuracy of reconstructed tractograms has been a longstanding challenge. Recently, deep learning methods have been applied to improve tractograms for better white matter coverage, but often comes at the expense of generating excessive false-positive connections. This is largely due to their reliance on local information to predict long range streamlines. To improve the accuracy of streamline propagation predictions, we introduce a novel deep learning framework that integrates image-domain spatial information and anatomical information along tracts, with the former extracted through convolutional layers and the later modeled via a Transformer-decoder. Additionally, we employ a weighted loss function to address fiber class imbalance encountered during training. We evaluate the proposed method on the simulated ISMRM 2015 Tractography Challenge dataset, achieving a valid streamline rate of 66.2%, white matter coverage of 63.8%, and successfully reconstructing 24 out of 25 bundles. Furthermore, on the multi-site Tractoinferno dataset, the proposed method demonstrates its ability to handle various diffusion MRI acquisition schemes, achieving a 5.7% increase in white matter coverage and a 4.1% decrease in overreach compared to RNN-based methods.
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.
Diffusion MRI (dMRI) is a unique imaging technique for in vivo characterization of tissue microstructure and white matter pathways. However, its relatively long acquisition time implies greater motion artifacts when imaging, for example, infants and Parkinson's disease patients. To accelerate dMRI acquisition, we propose in this paper (i) a diffusion encoding scheme, called Slice-Interleaved Diffusion Encoding (SIDE), that interleaves each diffusion-weighted (DW) image volume with slices that are encoded with different diffusion gradients, essentially allowing the slice-undersampling of image volume associated with each diffusion gradient to significantly reduce acquisition time, and (ii) a method based on deep learning for effective reconstruction of DW images from the highly slice-undersampled data. Evaluation based on the Human Connectome Project (HCP) dataset indicates that our method can achieve a high acceleration factor of up to 6 with minimal information loss. Evaluation using dMRI data acquired with SIDE acquisition demonstrates that it is possible to accelerate the acquisition by as much as 50 folds when combined with multi-band imaging.
Parcellation of whole-brain tractography streamlines is an important step for tract-based analysis of brain white matter microstructure. Existing fiber parcellation approaches rely on accurate registration between an atlas and the tractograms of an individual, however, due to large individual differences, accurate registration is hard to guarantee in practice. To resolve this issue, we propose a novel deep learning method, called DeepBundle, for registration-free fiber parcellation. Our method utilizes graph convolution neural networks (GCNNs) to predict the parcellation label of each fiber tract. GCNNs are capable of extracting the geometric features of each fiber tract and harnessing the resulting features for accurate fiber parcellation and ultimately avoiding the use of atlases and any registration method. We evaluate DeepBundle using data from the Human Connectome Project. Experimental results demonstrate the advantages of DeepBundle and suggest that the geometric features extracted from each fiber tract can be used to effectively parcellate the fiber tracts.