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Tractography traces the peak directions extracted from fiber orientation distribution (FOD) suffering from ambiguous spatial correspondences between diffusion directions and fiber geometry, which is prone to producing erroneous tracks while…
Constrained Spherical Deconvolution (CSD) is widely used to estimate the white matter fiber orientation distribution (FOD) from diffusion MRI data. Its angular resolution depends on the maximum spherical harmonic order ($l_{max}$): low…
The connectivity and structural integrity of the white matter of the brain is nowadays known to be implicated into a wide range of brain-related disorders. However, it was not before the advent of diffusion Magnetic Resonance Imaging (dMRI)…
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…
Diffusion-weighted magnetic resonance imaging (DW-MRI) is a critical imaging method for capturing and modeling tissue microarchitecture at a millimeter scale. A common practice to model the measured DW-MRI signal is via fiber orientation…
Due to recent technological advances, large brain imaging data sets can now be collected. Such data are highly complex so extraction of meaningful information from them remains challenging. Thus, there is an urgent need for statistical…
We present a novel method for estimation of the fiber orientation distribution (FOD) function based on diffusion-weighted Magnetic Resonance Imaging (D-MRI) data. We formulate the problem of FOD estimation as a regression problem through…
Fiber tractography is an important tool of computational neuroscience that enables reconstructing the spatial connectivity and organization of white matter of the brain. Fiber tractography takes advantage of diffusion Magnetic Resonance…
Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or conformational traps reflecting topological frustration…
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…
Partial Differential Equation (PDE)-based approaches have gained significant attention in image despeckling due to their strong capability to preserve structural details while suppressing noise. However, conventional second-order PDE models…
Tractography is typically performed for each subject using the diffusion tensor imaging (DTI) data in its native subject space rather than in some space common to the entire study cohort. Despite performing tractography on a population…
Data from diffusion magnetic resonance imaging (dMRI) can be used to reconstruct fiber tracts, for example, in muscle and white matter. Estimation of fiber orientations (FOs) is a crucial step in the reconstruction process and these…
We present a rotation-equivariant unsupervised learning framework for the sparse deconvolution of non-negative scalar fields defined on the unit sphere. Spherical signals with multiple peaks naturally arise in Diffusion MRI (dMRI), where…
Confocal histology provides an opportunity to establish intra-voxel fiber orientation distributions that can be used to quantitatively assess the biological relevance of diffusion weighted MRI models, e.g., constrained spherical…
White matter bundle segmentation is a cornerstone of modern tractography to study the brain's structural connectivity in domains such as neurological disorders, neurosurgery, and aging. In this study, we present FIESTA (FIbEr Segmentation…
We present DeepTract, a deep-learning framework for estimating white matter fibers orientation and streamline tractography. We adopt a data-driven approach for fiber reconstruction from diffusion weighted images (DWI), which does not assume…
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…
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…
Diffusion MRI is a well established imaging modality providing a powerful way to probe the structure of the white matter non-invasively. Despite its potential, the intrinsic long scan times of these sequences have hampered their use in…