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Magnetic Resonance Imaging (MRI) is essential for noninvasive generation of high-quality images of human tissues. Accurate segmentation of MRI data is critical for medical applications like brain anatomy analysis and disease detection.…

Purpose: To implement a brain segmentation pipeline based on convolutional neural networks, which rapidly segments 3D volumes into 27 anatomical structures. To provide an extensive, comparative study of segmentation performance on various…

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR…

Deep learning methods are the de-facto solutions to a multitude of medical image analysis tasks. Cardiac MRI segmentation is one such application which, like many others, requires a large number of annotated data so a trained network can…

Cardiac segmentation is a critical task in medical imaging, essential for detailed analysis of heart structures, which is crucial for diagnosing and treating various cardiovascular diseases. With the advent of deep learning, automated…

Tumor segmentation from multi-modal brain MRI images is a challenging task due to the limited samples, high variance in shapes and uneven distribution of tumor morphology. The performance of automated medical image segmentation has been…

Neuroimaging to neuropathology correlation (NTNC) promises to enable the transfer of microscopic signatures of pathology to in vivo imaging with MRI, ultimately enhancing clinical care. NTNC traditionally requires a volumetric MRI scan,…

Deep neural networks with multilevel connections process input data in complex ways to learn the information.A networks learning efficiency depends not only on the complex neural network architecture but also on the input training…

Deep learning models usually require sufficient training data to achieve high accuracy, but obtaining labeled data can be time-consuming and labor-intensive. Here we introduce a template-based training method to train a 3D U-Net model from…

Segmentation is a fundamental task in medical image analysis. The clinical interest is often to measure the volume of a structure. To evaluate and compare segmentation methods, the similarity between a segmentation and a predefined ground…

Accurate segmentation of brain tissue in magnetic resonance images (MRI) is a diffcult task due to different types of brain abnormalities. Using information and features from multimodal MRI including T1, T1-weighted inversion recovery…

Past few years have witnessed the prevalence of deep learning in many application scenarios, among which is medical image processing. Diagnosis and treatment of brain tumors requires an accurate and reliable segmentation of brain tumors as…

The segmentation of brain tumors in multimodal MRIs is one of the most challenging tasks in medical image analysis. The recent state of the art algorithms solving this task is based on machine learning approaches and deep learning in…

Recently, deep convolutional neural networks have achieved great success for medical image segmentation. However, unlike segmentation of natural images, most medical images such as MRI and CT are volumetric data. In order to make full use…

Fetal brain segmentation is an important first step for slice-level motion correction and slice-to-volume reconstruction in fetal MRI. Fast and accurate segmentation of the fetal brain on fetal MRI is required to achieve real-time fetal…

Purpose: Conventional automated segmentation of the head anatomy in MRI distinguishes different brain and non-brain tissues based on image intensities and prior tissue probability maps (TPM). This works well for normal head anatomies, but…

Semantic segmentation has become an important task in computer vision with the growth of self-driving cars, medical image segmentation, etc. Although current models provide excellent results, they are still far from perfect and while there…

Brain segmentation is a fundamental first step in neuroimage analysis. In the case of fetal MRI, it is particularly challenging and important due to the arbitrary orientation of the fetus, organs that surround the fetal head, and…

While emerging 3D medical foundation models are envisioned as versatile tools with offer general-purpose capabilities, their validation remains largely confined to regional and structural imaging, leaving a significant modality discrepancy…

Objective: Convolutional neural networks (CNNs) have demonstrated promise in automated cardiac magnetic resonance image segmentation. However, when using CNNs in a large real-world dataset, it is important to quantify segmentation…