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Representation learning has driven major advances in natural image analysis by enabling models to acquire high-level semantic features. In microscopy imaging, however, it remains unclear what current representation learning methods actually…
Functional MRI (fMRI) is widely used to examine brain functionality by detecting alteration in oxygenated blood flow that arises with brain activity. This work aims to investigate the neurological variation of human brain responses during…
As very large studies of complex neuroimaging phenotypes become more common, human quality assessment of MRI-derived data remains one of the last major bottlenecks. Few attempts have so far been made to address this issue with machine…
We adapt structural complexity analysis to three-dimensional signals, with an emphasis on brain magnetic resonance imaging (MRI). This framework captures the multiscale organization of volumetric data by coarse-graining the signal at…
Neuroimaging measures of the brain's white matter connections can enable the prediction of non-imaging phenotypes, such as demographic and cognitive measures. Existing works have investigated traditional microstructure and connectivity…
Segmentation has been a major task in neuroimaging. A large number of automated methods have been developed for segmenting healthy and diseased brain tissues. In recent years, deep learning techniques have attracted a lot of attention as a…
Small-animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition,…
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…
Deep learning models are often considered black boxes due to their complex hierarchical transformations. Identifying suitable architectures is crucial for maximizing predictive performance with limited data. Understanding the geometric…
The goal of diffusion-weighted magnetic resonance imaging (DWI) is to infer the structural connectivity of an individual subject's brain in vivo. To statistically study the variability and differences between normal and abnormal brain…
The brain structural connectome is generated by a collection of white matter fiber bundles constructed from diffusion weighted MRI (dMRI), acting as highways for neural activity. There has been abundant interest in studying how the…
The human brain cortical layer has a convoluted morphology that is unique to each individual. Characterization of the cortical morphology is necessary in longitudinal studies of structural brain change, as well as in discriminating…
Diffusion MRI measures of the human brain provide key insight into microstructural variations across individuals and into the impact of central nervous system diseases and disorders. One approach to extract information from diffusion…
Background: Quantitative susceptibility mapping (QSM) of the brain is an advanced MRI technique for assessing tissue characteristics based on magnetic susceptibility, which varies with the composition of the tissue, such as iron, calcium,…
Human perception plays a vital role in forming beliefs and understanding reality. A deeper understanding of brain functionality will lead to the development of novel deep neural networks. In this work, we introduce a novel framework named…
Computational models of biophysical tissue properties have been widely used in diffusion MRI (dMRI) research to elucidate the link between microstructural properties and MR signal formation. For brain tissue, the research community has…
In this study, we present a technique that spans multi-scale views (global scale -- meaning brain network-level and local scale -- examining each individual ROI that constitutes the network) applied to resting-state fMRI volumes. Deep…
The extraction of fibers from dMRI data typically produces a large number of fibers, it is common to group fibers into bundles. To this end, many specialized distance measures, such as MCP, have been used for fiber similarity. However,…
Quantitative, volumetric analysis of Magnetic Resonance Imaging (MRI) is a fundamental way researchers study the brain in a host of neurological conditions including normal maturation and aging. Despite the availability of open-source brain…
Recent cellular-level volumetric brain reconstructions have revealed high levels of anatomic complexity. Determining which structural aspects of the brain to focus on, especially when comparing with computational models and other organisms,…