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The development of automated tools for brain morphometric analysis in infants has lagged significantly behind analogous tools for adults. This gap reflects the greater challenges in this domain due to: 1) a smaller-scaled region of…

This study investigates a 3D and fully convolutional neural network (CNN) for subcortical brain structure segmentation in MRI. 3D CNN architectures have been generally avoided due to their computational and memory requirements during…

In this paper, we present an automated approach for segmenting multiple sclerosis (MS) lesions from multi-modal brain magnetic resonance images. Our method is based on a deep end-to-end 2D convolutional neural network (CNN) for slice-based…

Cytoarchitectonic parcellations of the human brain serve as anatomical references in multimodal atlas frameworks. They are based on analysis of cell-body stained histological sections and the identification of borders between brain areas.…

Automatic segmentation of brain MR images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is critical for tissue volumetric analysis and cortical surface reconstruction. Due to dramatic structural and appearance…

To achieve fast, robust, and accurate reconstruction of the human cortical surfaces from 3D magnetic resonance images (MRIs), we develop a novel deep learning-based framework, referred to as SurfNN, to reconstruct simultaneously both inner…

Accurate segmentation of brain tumors in MRI scans is critical for clinical diagnosis and treatment planning. We propose a semi-supervised, two-stage framework that extends the ReCoSeg approach to the larger and more heterogeneous BraTS…

Precise characterization of stroke lesions from MRI data has immense value in prognosticating clinical and cognitive outcomes following a stroke. Manual stroke lesion segmentation is time-consuming and requires the expertise of neurologists…

Purpose: To develop a truly calibrationless reconstruction method that derives ESPIRiT maps from uniformly-undersampled multi-channel MR data by deep learning. Methods: ESPIRiT, one commonly used parallel imaging reconstruction technique,…

Computational modeling of Multiresolution- Fractional Brownian motion (fBm) has been effective in stochastic multiscale fractal texture feature extraction and machine learning of abnormal brain tissue segmentation. Further, deep…

Whole-slide multiplex imaging of brain tissue generates massive information-dense images that are challenging to analyze and require custom software. We present an alternative query-driven programming-free strategy using a multiplex visual…

Purpose: To improve image quality and accelerate the acquisition of 3D MRF. Methods: Building on the multi-axis spiral-projection MRF technique, a subspace reconstruction with locally low rank (LLR) constraint and a modified…

Fetal cortical plate segmentation is essential in quantitative analysis of fetal brain maturation and cortical folding. Manual segmentation of the cortical plate, or manual refinement of automatic segmentations is tedious and…

Reliable MRI defacing techniques to safeguard patient privacy while preserving brain anatomy are critical for research collaboration. Existing methods often struggle with incomplete defacing or degradation of brain tissue regions. We…

Automatic segmentation of diverse heterogeneous brain lesions using multi-modal MRI is a challenging problem in clinical neuroimaging, mainly because of the lack of generalizability and high prediction variance of pathology-specific deep…

Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due…

Advances in image registration and machine learning have recently enabled volumetric analysis of postmortem brain tissue from conventional photographs of coronal slabs, which are routinely collected in brain banks and neuropathology…

We present MedicDeepLabv3+, a convolutional neural network that is the first completely automatic method to segment cerebral hemispheres in magnetic resonance (MR) volumes of rats with lesions. MedicDeepLabv3+ improves the state-of-the-art…

Registration is a core component of many imaging pipelines. In case of clinical scans, with lower resolution and sometimes substantial motion artifacts, registration can produce poor results. Visual assessment of registration quality in…

Accurate brain parcellation in diffusion MRI (dMRI) space is essential for advanced neuroimaging analyses. However, most existing approaches rely on anatomical MRI for segmentation and inter-modality registration, a process that can…