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The self-consistent field (SCF) generation of the three-dimensional (3D) electron density distribution ($\rho$) represents a fundamental aspect of density functional theory (DFT) and related first-principles calculations, and how one can…
Diffusion magnetic resonance imaging (dMRI) provides a unique tool for noninvasively probing the microstructure of the neuronal tissue. The NODDI model has been a popular approach to the estimation of tissue microstructure in many…
Diffusion MRI (dMRI) of the developing brain can provide valuable insights into the white matter development. However, slice thickness in fetal dMRI is typically high (i.e., 3-5 mm) to freeze the in-plane motion, which reduces the…
We suggest to utilize the rich information content about microstructural tissue properties entangled in asymmetric balanced steady-state free precession (bSSFP) profiles to estimate multiple diffusion metrics simultaneously by neural…
Magnetic Resonance Imaging (MRI) is widely used in the pathological and functional studies of the brain, such as epilepsy, tumor diagnosis, etc. Automated accurate brain tissue segmentation like cerebro-spinal fluid (CSF), gray matter (GM),…
Diffusion-weighted Magnetic Resonance Imaging (dMRI) is increasingly used to study the fetal brain in utero. An important computation enabled by dMRI is streamline tractography, which has unique applications such as tract-specific analysis…
Diffusion-weighted MRI is increasingly used to study the normal and abnormal development of fetal brain in-utero. Recent studies have shown that dMRI can offer invaluable insights into the neurodevelopmental processes in the fetal stage.…
We propose a 3D neural network with specific loss functions for quantitative computed tomography (QCT) noise reduction to compute micro-structural parameters such as tissue mineral density (TMD) and bone volume ratio (BV/TV) with…
Cell-level dense prediction is central to computational pathology, but remains challenging due to fine-grained histological structures, strong domain shifts, and costly dense annotations. Existing ViT-based pathology foundation models rely…
Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive volumetric studies and quantitative analysis of early brain developement. However, computing such segmentations is very challenging, especially for…
The rapid increment of morbidity of brain stroke in the last few years have been a driving force towards fast and accurate segmentation of stroke lesions from brain MRI images. With the recent development of deep-learning, computer-aided…
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…
Our understanding of the human connectome is fundamentally limited by the resolution of diffusion MR images. Reconstructing a connectome's constituent neural pathways with tractography requires following a continuous field of fiber…
Accurate detection and segmentation of brain tumors in magnetic resonance imaging (MRI) are critical for effective diagnosis and treatment planning. Despite advances in convolutional neural networks (CNNs) such as U-Net, existing models…
Brain tumor segmentation plays a pivotal role in medical image processing. In this work, we aim to segment brain MRI volumes. 3D convolution neural networks (CNN) such as 3D U-Net and V-Net employing 3D convolutions to capture the…
Models of diffusion MRI within a voxel are useful for making inferences about the properties of the tissue and inferring fiber orientation distribution used by tractography algorithms. A useful model must fit the data accurately. However,…
Diffusion magnetic resonance imaging is an imaging technology designed to probe anatomical architectures of biological samples in an in vivo and non-invasive manner through measuring water diffusion. The contribution of this paper is…
Multimode fibers (MMF) are an example of a highly scattering medium which scramble the coherent light propagating within them and produce seemingly random patterns. Thus, for applications such as imaging and image projection through a MMF,…
Deformable image registration is fundamental to longitudinal and population analysis. Geometric alignment of the infant brain MR images is challenging, owing to rapid changes in image appearance in association with brain development. In…
Fiber tracking based on diffusion weighted Magnetic Resonance Imaging (dMRI) allows for noninvasive reconstruction of fiber bundles in the human brain. In this chapter, we discuss sources of error and uncertainty in this technique, and…