Lauren Jean O'Donnell

• PhD
• Professor (Assistant) at Harvard Medical School

The structural connections of the brain’s white matter are critical for brain function. Diffusion MRI tractography enables the in-vivo reconstruction of white matter fiber bundles and the study of their relationship to covariates of interest, such as neurobehavioral or clinical factors. In this work, we introduce Fiber Microstructure Quantile (FMQ)...

Tractography parcellation classifies streamlines reconstructed from diffusion MRI into anatomically defined fiber tracts for clinical and research applications. However, clinical scans often have incomplete fields of view (FOV) where brain regions are partially imaged, leading to partial, or truncated fiber tracts. To address this challenge, we int...

The shape of the brain's white matter connections is relatively unexplored in diffusion magnetic resonance imaging (dMRI) tractography analysis. While it is known that tract shape varies in populations and across the human lifespan, it is unknown if the variability in dMRI tractography‐derived shape may relate to the brain's functional variability...

Essential tremor (ET) is a common movement disorder with a strong genetic basis. Magnetic resonance imaging (MRI), particularly diffusion‐weighted MRI (dMRI) and T1 MRI, have been used to identify brain abnormalities of ET patients. However, the mechanisms by which genetic risk affects the brain to render individuals vulnerable to ET remain unknown...

The fine-grained segmentation of cerebellar structures is an essential step towards supplying increasingly accurate anatomically informed analyses, including, for example, white matter diffusion magnetic resonance imaging (MRI) tractography. Cerebellar tissue segmentation is typically performed on structural magnetic resonance imaging data, such as...

Brain nuclei are clusters of anatomically distinct neurons that serve as important hubs for processing and relaying information in various neural circuits. Fine-scale parcellation of the brain nuclei is vital for a comprehensive understanding of its anatomico-functional correlations. Diffusion MRI tractography is an advanced imaging technique that...

3D neuroimages provide a comprehensive view of brain structure and function, aiding in precise localization and functional connectivity analysis. Segmentation of white matter (WM) tracts using 3D neuroimages is vital for understanding the brain's structural connectivity in both healthy and diseased states. One-shot Class Incremental Semantic Segmen...

Diffusion MRI (dMRI) plays a crucial role in studying brain white matter connectivity. Cortical surface reconstruction (CSR), including the inner whiter matter (WM) and outer pial surfaces, is one of the key tasks in dMRI analyses such as fiber tractography and multimodal MRI analysis. Existing CSR methods rely on anatomical T1-weighted data and ma...

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 th...

Anorexia nervosa (AN) is linked to changes in autonomic function, but the specific neuroanatomical substrates of these changes are not well understood. In this study, we used diffusion-weighted imaging to examine white matter structure in the ventromedial prefrontal cortex–dorsal vagal complex (vmPFC-DVC) pathway, which is essential for autonomic r...

Tractography parcellation classifies streamlines reconstructed from diffusion MRI into anatomically defined fiber tracts for clinical and research applications. However, clinical scans often have incomplete fields of view (FOV) where brain regions are partially imaged, leading to partial or truncated fiber tracts. To address this challenge, we intr...

Medical image registration is a fundamental task in medical image analysis, aiming to establish spatial correspondences between paired images. However, existing unsupervised deformable registration methods rely solely on intensity-based similarity metrics, lacking explicit anatomical knowledge, which limits their accuracy and robustness. Vision fou...

The cerebellum, long implicated in movement, is now recognized as a contributor to higher-order cognition. The cerebellar pathways provide key structural links between the cerebellum and cerebral regions integral to language, memory, and executive function. Here, we present a large-scale, cross-sectional diffusion MRI (dMRI) analysis investigating...

The retinogeniculate visual 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 the treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced...

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...

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...

Reconstructing neuron morphology from 3D light microscope imaging data is critical to aid neuroscientists in analyzing brain networks and neuroanatomy. With the boost from deep learning techniques, a variety of learning-based segmentation models have been developed to enhance the signal-to-noise ratio of raw neuron images as a pre-processing step i...

The structural connections of the brain's white matter are critical for brain function. Diffusion MRI tractography enables the in-vivo reconstruction of white matter fiber bundles and the study of their relationship to covariates of interest, such as neurobehavioral or clinical factors. In this work, we introduce Fiber Microstructure Quantile (FMQ)...

The shape of the brain's white matter connections is relatively unexplored in diffusion MRI tractography analysis. While it is known that tract shape varies in populations and across the human lifespan, it is unknown if the variability in dMRI tractography-derived shape may relate to the brain's functional variability across individuals. This work...

The superficial white matter (SWM) consists of numerous short‐range association fibers connecting adjacent and nearby gyri and plays an important role in brain function, development, aging, and various neurological disorders. Diffusion MRI (dMRI) tractography is an advanced imaging technique that enables in vivo mapping of the SWM. However, detaile...

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. Using EVENet, we obtained accurate parcellation a...

Hypothesis This study investigates the impact of different diffusion magnetic imaging (dMRI) acquisition settings and mathematical fiber models on tractography performance for depicting cranial nerve (CN) VII in healthy young adults. Background The aim of this study is to optimize visualization of CN VII for preoperative assessment in surgeries ne...

Parcellation of human cerebellar pathways is essential for advancing our understanding of the human brain. Existing diffusion magnetic resonance imaging tractography parcellation methods have been successful in defining major cerebellar fibre tracts, while relying solely on fibre tract structure. However, each fibre tract may relay information rela...

Diffusion MRI (dMRI) is an advanced imaging technique characterizing tissue microstructure and white matter structural connectivity of the human brain. The demand for high-quality dMRI data is growing, driven by the need for better resolution and improved tissue contrast. However, acquiring high-quality dMRI data is expensive and time-consuming. In...

Parcellation of white matter tractography provides anatomical features for disease prediction, anatomical tract segmentation, surgical brain mapping, and non-imaging phenotype classifications. However, parcellation does not always reach 100% accuracy due to various factors, including inter-individual anatomical variability and the quality of neuroi...

Parcellation of human cerebellar pathways is essential for advancing our understanding of the human brain. Existing diffusion MRI tractography parcellation methods have been successful in defining major cerebellar fibre tracts, while relying solely on fibre tract structure. However, each fibre tract may relay information related to multiple cogniti...

The study of brain differences across Eastern and Western populations provides vital insights for understanding potential cultural and genetic influences on cognition and mental health. Diffusion MRI (dMRI) tractography is an important tool in assessing white matter (WM) connectivity and brain tissue microstructure across different populations. How...

Essential tremor (ET) is a common movement disorder with a strong genetic basis. Magnetic resonance imaging (MRI), particularly diffusion-weighted MRI (dMRI) and T1 MRI has been used to identify brain abnormalities of ET patients. However, the mechanisms by which genetic risk affects the brain to render individuals vulnerable to ET remain unknown....

The relationship between brain connections and non-imaging phenotypes is increasingly studied using deep neural networks. However, the local and global properties of the brain's white matter networks are often overlooked in convolutional network design. We introduce TractGraphFormer, a hybrid Graph CNN-Transformer deep learning framework tailored f...

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 a novel deep regression method, namely TractoSCR, that allows full supervision for contrastive learning in...

Background Mild traumatic brain injury (mTBI) is common in children. Long-term cognitive and behavioral outcomes as well as underlying structural brain alterations following pediatric mTBI have yet to be determined. In addition, the effect of age-at-injury on long-term outcomes is largely unknown. Methods Children with a history of mTBI ( n = 406;...

Objective Impaired visuospatial memory is a clinical feature in individuals with neuropathologically confirmed chronic traumatic encephalopathy (CTE) post-mortem. Altered white matter microstructure in the cingulum bundle (CB) has previously been associated with impaired visuospatial memory in other neurodegenerative disorders. The aim of this stud...

The retinogeniculate visual 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 the treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced...

Motivation: The prediction of cognitive performance scores using diffusion MRI tractography enables the study of relationships between brain structure and function. Goal(s): Our goal is to achieve accurate prediction of cognition and identify critical brain regions for prediction. Approach: We propose a geometric deep-learning framework for languag...

Motivation: Existing white matter atlases are usually created based on a certain population, which may omit subtle differences across populations from different cultures. Goal(s): This study presents a fine-scale white matter atlas that is created concurrently using high-quality diffusion MRI data from both Eastern and Western populations. Approa...

Regular participation in sports results in a series of physiological adaptations. However, little is known about the brain adaptations to physical activity. Here we aimed to investigate whether young endurance athletes and non-athletes differ in the gray and white matter of the brain and whether cardiorespiratory fitness (CRF) is associated with th...

Parcellation of anatomically segregated cortical and subcortical brain regions is required in diffusion MRI (dMRI) analysis for region-specific quantification and better anatomical specificity of tractography. Most current dMRI parcellation approaches compute the parcellation from anatomical MRI (T1- or T2-weighted) data, using tools such as FreeSu...

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. The CST exhibits a somatotopic organization, which means that the motor neurons that control specific body parts are arranged in order within the CST. Diffusion magnetic resonance imaging (MRI)...

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 h...

Objective To investigate how the presence/side of hippocampal sclerosis (HS) are related to the white matter structure of cingulum bundle (CB), arcuate fasciculus (AF), and inferior longitudinal fasciculus (ILF) in mesial temporal lobe epilepsy (MTLE). Methods We acquired diffusion‐weighted magnetic resonance imaging (MRI) from 86 healthy and 71 i...

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 h...

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 informatio...

The Adolescent Brain Cognitive Development (ABCD) study is a groundbreaking effort aimed at providing a comprehensive understanding of adolescent brain development. With data collected from over 10,000 children across 21 sites, this study promises to unlock key insights into the cognitive, behavioral, and neuroimaging data that underpins this criti...

Diffusion MRI tractography is an advanced imaging technique that enables in vivo mapping of the brain's white matter connections. White matter parcellation classifies tractography streamlines into clusters or anatomically meaningful tracts. It enables quantification and visualization of whole-brain tractography. Currently, most parcellation methods...

White matter fiber clustering is an important strategy for white matter parcellation, which enables quantitative analysis of brain connections in health and disease. In combination with expert neuroanatomical labeling, data-driven white matter fiber clustering is a powerful tool for creating atlases that can model white matter anatomy across indivi...

Background: Diffusion magnetic resonance imaging white matter tractography, an increasingly popular preoperative planning modality used for pre-surgical planning in brain tumor patients, is employed with the goal of maximizing tumor resection while sparing postoperative neurological function. Clinical translation of white matter tractography has b...

A complete structural definition of the human nervous system must include delineation of its wiring diagram (e.g., [1]). The complete formulation of the human brain circuit diagram (BCD; [2]) has been hampered by an inability to determine connections in their entirety (i.e., not only pathway stems, but also origins and terminations). From a structu...

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 annotat...

Sleep disturbances are strongly associated with mild traumatic brain injury (mTBI) and post-traumatic stress disorder (PTSD). PTSD and mTBI have been linked to alterations in white matter (WM) microstructure, but whether poor sleep quality has a compounding effect on WM remains largely unknown. We evaluated sleep and diffusion magnetic resonance im...

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 bund...

Background: Moyamoya is a disease with progressive cerebral arterial stenosis leading to stroke and silent infarct. Diffusion-weighted magnetic resonance imaging (dMRI) studies show that adults with moyamoya have significantly lower fractional anisotropy (FA) and higher mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) com...

Segmentation of white matter tracts in diffusion magnetic resonance images is an important first step in many imaging studies of the brain in health and disease. Similar to medical image segmentation in general, a popular approach to white matter tract segmentation is to use U-Net based artificial neural network architectures. Despite many suggeste...

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 ta...

We present a novel deep learning framework, DeepRGVP, for the retinogeniculate pathway (RGVP) identification from dMRI tractography data. We propose a novel microstructure-supervised contrastive learning method (MicroSCL) that leverages both streamline labels and tissue microstructure (fractional anisotropy) for RGVP and non-RGVP. We propose a simp...

Large datasets often contain multiple distinct feature sets, or views, that offer complementary information that can be exploited by multi-view learning methods to improve results. We investigate anatomical-multi-view data, where each brain anatomical structure is described with multiple feature sets. In particular, we focus on sets of white matter...

We tested the null hypothesis that, after mild traumatic brain injury (mTBI), white matter changes near cerebral microbleeds (CMBs) are associated with cognitive decline. Magnetic resonance images were acquired from 62 adults with mTBI and from 203 matched healthy controls. A week post-injury, mTBI participants had 2.7±2.6 traumatic CMBs in WM, loc...

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 matr...

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 met...

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-le...

Background: Military service members are at increased risk for mental health issues and comorbidity with mild traumatic brain injury (mTBI) is common. Largely overlapping symptoms between conditions suggest a shared pathophysiology. The present work investigates the associations between white matter microstructure, psychological functioning, and s...

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 co...

Diffusion MRI tractography is an advanced imaging technique for quantitative mapping of the brain’s structural connectivity. Whole brain tractography (WBT) data contains over hundreds of thousands of individual fiber streamlines (estimated brain connections), and this data is usually parcellated to create compact representations for data analysis a...

White matter tract microstructure has been shown to influence neuropsychological scores of cognitive performance. However, prediction of these scores from white matter tract data has not been attempted. In this paper, we propose a deep-learning-based framework for neuropsychological score prediction using microstructure measurements estimated from...

Background Alterations in brain connectivity may underlie neuropsychiatric conditions such as schizophrenia. We here assessed the degree of convergence of frontostriatal fiber projections in 56 young adult healthy controls (HCs) and 108 matched Early Psychosis-Non-Affective patients (EP-NAs) using our novel fiber cluster analysis of whole brain dif...

Objectives: Disrupted auditory networks play an important role in the pathophysiology of psychosis, with abnormalities already observed in individuals at clinical high-risk for psychosis (CHR). Here, we examine structural and functional connectivity of an auditory network in CHR utilising state-of-the-art electroencephalography and diffusion imagin...

To explore how cerebral microbleeds (CMBs) accompanying mild traumatic brain injury (mTBI) reflect white matter (WM) degradation and cognitive decline, magnetic resonance images were acquired from 62 mTBI adults (imaged ∼7 days and ∼6 months post-injury) and 203 matched healthy controls. On average, mTBI participants had a count of 2.7±2.6 traumati...

Diffusion MRI tractography is an advanced imaging technique that enables in vivo mapping of the brain's white matter connections. White matter parcellation classifies tractography streamlines into clusters or anatomically meaningful tracts. It enables quantification and visualization of whole-brain tractography. Currently, most parcellation methods...

White matter hyperintensities (WMH) are a typical feature of cerebral small vessel disease (CSVD), which contributes to about 50% of dementias worldwide. Microstructural alterations in deep white matter (DWM) have been widely examined in CSVD. However, little is known about abnormalities in superficial white matter (SWM) and their relevance for pro...

Diffusion MRI tractography is an advanced imaging technique for quantitative mapping of the brain's structural connectivity. Whole brain tractography (WBT) data contains over hundreds of thousands of individual fiber streamlines (estimated brain connections), and this data is usually parcellated to create compact representations for data analysis a...

White matter tract microstructure has been shown to influence neuropsychological scores of cognitive performance. However, prediction of these scores from white matter tract data has not been attempted. In this paper, we propose a deep-learning-based framework for neuropsychological score prediction using microstructure measurements estimated from...

Previous investigations of human cerebellar structure and function frequently reveal relationships between the cerebellum and executive functioning. Additionally, axon tracing investigations in primates demonstrate cerebellar connections with the prefrontal cortex, a region most classically associated with executive processes, via the thalamus. How...

White matter fiber clustering (WMFC) parcellates tractography data into anatomically meaningful fiber bundles, usually in an unsupervised manner without the need of labeled ground truth data. While widely used WMFC approaches have shown good performance using classical machine learning techniques, recent advances in deep learning reveal a promising...

We assess microstructural alterations in superficial white matter (SWM) in cerebral small vessel disease (CSVD) and evaluate their contributions to the decline in processing speed, which is the main dysfunction in CSVD. We identify that the significant decline in processing speed may relate to the involvement of WMH in the SWM under high burden of...

We present a large-scale harmonized dMRI study where we have performed successful white matter (WM) tractography parcellation across ~10k subjects from the ABCD study. We first assess the effects of data harmonization on WM parcellation, followed by an evaluation of WM parcellation using the entire harmonized dataset. We show that after harmonizati...

We present a novel deep learning method, DDMReg, for accurate dMRI registration. In dMRI registration, the goal is to align brain anatomical structures while ensuring local fiber orientations consistency with the underlying white matter anatomy. DDMReg is an unsupervised method for deformable dMRI registration, without the need of non-rigidly pre-r...

We propose a deep-learning-based framework, Superficial White Matter Analysis (SupWMA), which performs an efficient and consistent parcellation of 198 SWM clusters from whole-brain tractography. A point-cloud-based network is developed for our SWM parcellation task, and supervised contrastive learning enables more discriminative representations bet...

Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging technique that enables in vivo reconstruction of the brain’s white matter connections at macro scale. It provides an important tool for quantitative mapping of the brain’s structural connectivity using measures of connectivity or tissue microstructure. Over the last two...