The amygdala plays a vital role in emotional processing and exhibits structural diversity that necessitates fine-scale parcellation for a comprehensive understanding of its anatomico-functional correlations. Diffusion MRI tractography is an advanced imaging technique that can estimate the brain's white matter structural connectivity to potentially reveal the topography of the amygdala for studying its subdivisions. In this work, we present a deep clustering pipeline to perform automated, fine-scale parcellation of the amygdala using diffusion MRI tractography. First, we incorporate a newly proposed deep learning approach to enable accurate segmentation of the amygdala directly on the dMRI data. Next, we design a novel streamline clustering-based structural connectivity feature for a robust representation of voxels within the amygdala. Finally, we improve the popular joint dimensionality reduction and k-means clustering approach to enable amygdala parcellation at a finer scale. With the proposed method, we obtain nine unique amygdala parcels. Experiments show that these parcels can be consistently identified across subjects and have good correspondence to the widely used coarse-scale amygdala parcellation.
Diffusion MRI tractography parcellation classifies streamlines into anatomical fiber tracts to enable quantification and visualization for clinical and scientific applications. Current tractography parcellation methods rely heavily on registration, but registration inaccuracies can affect parcellation and the computational cost of registration is high for large-scale datasets. Recently, deep-learning-based methods have been proposed for tractography parcellation using various types of representations for streamlines. However, these methods only focus on the information from a single streamline, ignoring geometric relationships between the streamlines in the brain. We propose TractCloud, a registration-free framework that performs whole-brain tractography parcellation directly in individual subject space. We propose a novel, learnable, local-global streamline representation that leverages information from neighboring and whole-brain streamlines to describe the local anatomy and global pose of the brain. We train our framework on a large-scale labeled tractography dataset, which we augment by applying synthetic transforms including rotation, scaling, and translations. We test our framework on five independently acquired datasets across populations and health conditions. TractCloud significantly outperforms several state-of-the-art methods on all testing datasets. TractCloud achieves efficient and consistent whole-brain white matter parcellation across the lifespan (from neonates to elderly subjects, including brain tumor patients) without the need for registration. The robustness and high inference speed of TractCloud make it suitable for large-scale tractography data analysis. Our project page is available at https://tractcloud.github.io/.
We propose a geometric deep-learning-based framework, TractGeoNet, for performing regression using diffusion magnetic resonance imaging (dMRI) tractography and associated pointwise tissue microstructure measurements. By employing a point cloud representation, TractGeoNet can directly utilize pointwise tissue microstructure and positional information from all points within a fiber tract. To improve regression performance, we propose a novel loss function, the Paired-Siamese Regression loss, which encourages the model to focus on accurately predicting the relative differences between regression label scores rather than just their absolute values. In addition, we propose a Critical Region Localization algorithm to identify highly predictive anatomical regions within the white matter fiber tracts for the regression task. We evaluate the effectiveness of the proposed method by predicting individual performance on two neuropsychological assessments of language using a dataset of 20 association white matter fiber tracts from 806 subjects from the Human Connectome Project. The results demonstrate superior prediction performance of TractGeoNet compared to several popular regression models. Of the twenty tracts studied, we find that the left arcuate fasciculus tract is the most highly predictive of the two studied language performance assessments. The localized critical regions are widespread and distributed across both hemispheres and all cerebral lobes, including areas of the brain considered important for language function such as superior and anterior temporal regions, pars opercularis, and precentral gyrus. Overall, TractGeoNet demonstrates the potential of geometric deep learning to enhance the study of the brain's white matter fiber tracts and to relate their structure to human traits such as language performance.
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.
White matter (WM) tract segmentation based on diffusion magnetic resonance imaging (dMRI) plays an important role in the analysis of human health and brain diseases. However, the annotation of WM tracts is time-consuming and needs experienced neuroanatomists. In this study, to explore tract segmentation in the challenging setting of minimal annotations, we propose a novel framework utilizing only one annotated subject (subject-level one-shot) for tract segmentation. Our method is constructed by proposed registration-based peak augmentation (RPA) and uncertainty-based refining (URe) modules. RPA module synthesizes pseudo subjects and their corresponding labels to improve the tract segmentation performance. The proposed URe module alleviates the negative influence of the low-confidence voxels on pseudo subjects. Experimental results show that our method outperforms other state-of-the-art methods by a large margin, and our proposed modules are effective. Overall, our method achieves accurate whole-brain tract segmentation with only one annotated subject. Our code is available at https://github.com/HaoXu0507/ISBI2023-One-Shot-WM-Tract-Segmentation.
Superficial white matter (SWM) has been less studied than long-range connections despite being of interest to clinical research, andfew tractography parcellation methods have been adapted to SWM. Here, we propose an efficient geometry-based parcellation method (GeoLab) that allows high-performance segmentation of hundreds of short white matter bundles from a subject. This method has been designed for the SWM atlas of EBRAINS European infrastructure, which is composed of 657 bundles. The atlas projection relies on the precomputed statistics of six bundle-specific geometrical properties of atlas streamlines. In the spirit of RecoBundles, a global and local streamline-based registration (SBR) is used to align the subject to the atlas space. Then, the streamlines are labeled taking into account the six geometrical parameters describing the similarity to the streamlines in the model bundle. Compared to other state-of-the-art methods, GeoLab allows the extraction of more bundles with a higher number of streamlines.
The structure and variability of the brain's connections can be investigated via prediction of non-imaging phenotypes using neural networks. However, known neuroanatomical relationships between input features are generally ignored in network design. We propose TractGraphCNN, a novel, anatomically informed graph CNN framework for machine learning tasks using diffusion MRI tractography. An EdgeConv module aggregates features from anatomically similar white matter connections indicated by graph edges, and an attention module enables interpretation of predictive white matter tracts. Results in a sex prediction testbed task demonstrate strong performance of TractGraphCNN in two large datasets (HCP and ABCD). Graphs informed by white matter geometry demonstrate higher performance than graphs informed by gray matter connectivity. Overall, the bilateral cingulum and left middle longitudinal fasciculus are consistently highly predictive of sex. This work shows the potential of incorporating anatomical information, especially known anatomical similarities between input features, to guide convolutions in neural networks.
As the largest human cerebellar nucleus, the dentate nucleus (DN) functions significantly in the communication between the cerebellum and the rest of the brain. Structural connectivity-based parcellation has the potential to reveal the topography of the DN and enable the study of its subregions. In this paper, we investigate a deep nonnegative matrix factorization clustering method (DNMFC) for parcellation of the human DN based on its structural connectivity using diffusion MRI tractography. We propose to describe the connectivity of the DN using a set of curated tractography fiber clusters within the cerebellum. Experiments are conducted on the diffusion MRI data of 50 healthy adults from the Human Connectome Project. In comparison with state-of-the-art clustering methods, DN parcellations resulting from DNMFC show better quality and consistency of parcels across subjects.
The brain's white matter (WM) undergoes developmental and degenerative processes during the human lifespan. To investigate the relationship between WM anatomical regions and age, we study diffusion magnetic resonance imaging tractography that is finely parcellated into fiber clusters in the deep, superficial, and cerebellar WM. We propose a deep-learning-based age prediction model that leverages large convolutional kernels and inverted bottlenecks. We improve performance using novel discrete multi-faceted mix data augmentation and a novel prior-knowledge-based loss function that encourages age predictions in the expected range. We study a dataset of 965 healthy young adults (22-37 years) derived from the Human Connectome Project (HCP). Experimental results demonstrate that the proposed model achieves a mean absolute error of 2.59 years and outperforms compared methods. We find that the deep WM is the most informative for age prediction in this cohort, while the superficial WM is the least informative. Overall, the most predictive WM tracts are the thalamo-frontal tract from the deep WM and the intracerebellar input and Purkinje tract from the cerebellar WM.
Neuroimaging-based prediction of neurocognitive measures is valuable for studying how the brain's structure relates to cognitive function. However, the accuracy of prediction using popular linear regression models is relatively low. We propose Supervised Contrastive Regression (SCR), a simple yet effective method that allows full supervision for contrastive learning in regression tasks. SCR performs supervised contrastive representation learning by using the absolute difference between continuous regression labels (i.e. neurocognitive scores) to determine positive and negative pairs. We apply SCR to analyze a large-scale dataset including multi-site harmonized diffusion MRI and neurocognitive data from 8735 participants in the Adolescent Brain Cognitive Development (ABCD) Study. We extract white matter microstructural measures using a fine parcellation of white matter tractography into fiber clusters. We predict three scores related to domains of higher-order cognition (general cognitive ability, executive function, and learning/memory). To identify important fiber clusters for prediction of these neurocognitive scores, we propose a permutation feature importance method for high-dimensional data. We find that SCR improves the accuracy of neurocognitive score prediction compared to other state-of-the-art methods. We find that the most predictive fiber clusters are predominantly located within the superficial white matter and projection tracts, particularly the superficial frontal white matter and striato-frontal connections. Overall, our results demonstrate the utility of contrastive representation learning methods for regression, and in particular for improving neuroimaging-based prediction of higher-order cognitive abilities.