DeepNuParc: A novel deep clustering framework for fine-scale parcellation of brain nuclei using diffusion MRI tractography.

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 their 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 nuclei of interest for studying their subdivisions.

Fiber microstructure quantile (FMQ) regression: A novel statistical approach for analyzing white matter bundles from periphery to core.

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) Regression, a new statistical approach for studying the association between white matter fiber bundles and scalar factors (e.

The superficial white matter in language processing: Broca's area connections are bilaterally associated with individual performance in children and adults.

While deeper white matter connections, such as the arcuate fasciculus and frontal aslant tract, are well known for their role in language and show leftward asymmetries in adults, the contribution of the short-range cortico-cortical superficial white matter (SWM) connections remains less understood. In this preregistered study, we examined white matter connections of Broca's area and its right hemisphere homolog in early adolescents and young adults using two large, publicly available datasets: the Adolescent Brain Cognitive Development Study and the Human Connectome Project Young Adult Study, totaling over 10,000 participants. We anatomically curated the O'Donnell Research Group (ORG) tractography atlas to identify SWM fiber clusters intersecting Broca's area (pars opercularis and pars triangularis), confirmed through expert visual inspection.

Association of Superficial White Matter Microstructure With Cortical Pathology Deposition Across Early Stages of the AD Continuum.

Background And Objectives: β-amyloid (Aβ) and tau, 2 prominent pathologies of Alzheimer disease (AD), originate in cortical regions and primarily affect, and even spread along, the white matter tracts directly connected to these cortical regions. Superficial white matter (SWM), containing short-range association connections beneath the cortex, has been affected in mild cognitive impairment and AD, with gaps in understanding the disease's early stages. We perform a detailed investigation of individual SWM connections with cortical pathology deposition and cognition in the early stages of the AD continuum.

High-resolution segmentation of the cavum septum pellucidum in young adult human brains.

The cavum septum pellucidum (CSP) is a small cerebrospinal fluid-filled space found between the lateral ventricles of the forebrain that is often used as a biomarker for neurological disease and brain injury. The incidence of the CSP varies widely in different studies, with many reports finding that the CSP is frequently absent in healthy brains. Variables such as race, age and sex are typically not well-reported in CSP studies, presenting a challenge to understanding the normal distribution of the CSP in adult human brains.

Brain connectivity: complex, not chaotic.

The term "connections" is a commonly used and convenient shorthand for describing the complex organization of the brain, but it can easily lead to an overemphasis on pairwise or point-to-point, source-target network connectivity. Anatomical studies make clear that there are other important features to consider such as divergence and collateralization (axons or bundles branching to multiple targets), convergence (multiple bundles from different sources converging on the same target), and scrambled topography along a trajectory. This short "Did You Know" communication elaborates on several of these features from the anatomical perspective, while inviting continued dialogue with the tractography community in addressing the shared goals of better understanding brain organization.

Towards an informed choice of diffusion MRI image contrasts for cerebellar segmentation.

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 T1-weighted data, while connectivity between segmented regions is mapped using diffusion MRI tractography data. Small deviations in structural to diffusion MRI data co-registration may negatively impact connectivity analyses.

The Shape of the Brain's Connections Is Predictive of Cognitive Performance: An Explainable Machine Learning Study.

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 across individuals. This work explores the potential of leveraging tractography fiber cluster shape measures to predict subject-specific cognitive performance.

The shape of the brain's connections is predictive of cognitive performance: an explainable machine learning study.

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 explores the potential of leveraging tractography fiber cluster shape measures to predict subject-specific cognitive performance.

Consistent cerebellar pathway-cognition associations across pre-adolescents & young adults: a diffusion MRI study of 9000+ participants.

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 relationships between cerebellar pathway microstructure and cognitive performance in over 9,000 participants spanning pre-adolescence (n>8,000 from the ABCD dataset) and young adulthood (n>900 from the HCP-YA dataset).

TractGraphFormer: Anatomically informed hybrid graph CNN-transformer network for interpretable sex and age prediction from diffusion MRI tractography.

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 for diffusion MRI tractography.

Assessment of the Depiction of Superficial White Matter Using Ultra-High-Resolution Diffusion MRI.

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, detailed imaging of the small, highly-curved fibers of the SWM is a challenge for current clinical and research dMRI acquisitions.

Deep multimodal saliency parcellation of cerebellar pathways: Linking microstructure and individual function through explainable multitask learning.

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 related to multiple cognitive and motor functions of the cerebellum.

A diffusion MRI tractography atlas for concurrent white matter mapping across Eastern and Western populations.

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. However, a comprehensive investigation into WM fiber tracts between Eastern and Western populations is challenged due to the lack of a cross-population WM atlas and the large site-specific variability of dMRI data.

Investigation of brain iron in anorexia nervosa, a quantitative susceptibility mapping study.

Background: Anorexia nervosa (AN) is a potentially fatal psychiatric condition, associated with structural brain changes such as gray matter volume loss. The pathophysiological mechanisms for these changes are not yet fully understood. Iron is a crucial element in the development and function of the brain.

A preliminary choroid plexus volumetric study in individuals with psychosis.

The choroid plexus (ChP) is part of the blood-cerebrospinal fluid barrier, regulating brain homeostasis and the brain's response to peripheral events. Its upregulation and enlargement are considered essential in psychosis. However, the timing of the ChP enlargement has not been established.

In Vivo 7-Tesla MRI Investigation of Brain Iron and Its Metabolic Correlates in Chronic Schizophrenia.

Brain iron is central to dopaminergic neurotransmission, a key component in schizophrenia pathology. Iron can also generate oxidative stress, which is one proposed mechanism for gray matter volume reduction in schizophrenia. The role of brain iron in schizophrenia and its potential link to oxidative stress has not been previously examined.

Anatomically curated segmentation of human subcortical structures in high resolution magnetic resonance imaging: An open science approach.

Magnetic resonance imaging (MRI)-based brain segmentation has recently been revolutionized by deep learning methods. These methods use large numbers of annotated segmentations to train algorithms that have the potential to perform brain segmentations reliably and quickly. However, training data for these algorithms are frequently obtained from automated brain segmentation systems, which may contain inaccurate neuroanatomy.

Volumetric Analysis of Amygdala and Hippocampal Subfields for Infants with Autism.

Previous studies have demonstrated abnormal brain overgrowth in children with autism spectrum disorder (ASD), but the development of specific brain regions, such as the amygdala and hippocampal subfields in infants, is incompletely documented. To address this issue, we performed the first MRI study of amygdala and hippocampal subfields in infants from 6 to 24 months of age using a longitudinal dataset. A novel deep learning approach, Dilated-Dense U-Net, was proposed to address the challenge of low tissue contrast and small structural size of these subfields.

The association of matrix metalloproteinase 9 (MMP9) with hippocampal volume in schizophrenia: a preliminary MRI study.

Matrix metalloproteinases 9 (MMP9) are enzymes involved in regulating neuroplasticity in the hippocampus. This, combined with evidence for disrupted hippocampal structure and function in schizophrenia, has prompted our current investigation into the relationship between MMP9 and hippocampal volumes in schizophrenia. 34 healthy individuals (mean age = 32.

MRI-based Parcellation and Morphometry of the Individual Rhesus Monkey Brain: the macaque Harvard-Oxford Atlas (mHOA), a translational system referencing a standardized ontology.

Investigations of the rhesus monkey (Macaca mulatta) brain have shed light on the function and organization of the primate brain at a scale and resolution not yet possible in humans. A cornerstone of the linkage between non-human primate and human studies of the brain is magnetic resonance imaging, which allows for an association to be made between the detailed structural and physiological analysis of the non-human primate and that of the human brain. To further this end, we present a novel parcellation method and system for the rhesus monkey brain, referred to as the macaque Harvard-Oxford Atlas (mHOA), which is based on the human Harvard-Oxford Atlas (HOA) and grounded in an ontological and taxonomic framework.