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Whole brain segmentation from structural magnetic resonance imaging (MRI) is a prerequisite for most morphological analyses, but is computationally intense and can therefore delay the availability of image markers after scan acquisition. We…
Medical images used in clinical practice are heterogeneous and not the same quality as scans studied in academic research. Preprocessing breaks down in extreme cases when anatomy, artifacts, or imaging parameters are unusual or protocols…
Segmenting a structural magnetic resonance imaging (MRI) scan is an important pre-processing step for analytic procedures and subsequent inferences about longitudinal tissue changes. Manual segmentation defines the current gold standard in…
Objectives: High classification accuracy of Alzheimer's disease (AD) from structural MRI has been achieved using deep neural networks, yet the specific image features contributing to these decisions remain unclear. In this study, the…
Brain extraction or whole brain segmentation is an important first step in many of the neuroimage analysis pipelines. The accuracy and robustness of brain extraction, therefore, is crucial for the accuracy of the entire brain analysis…
Human brain development is rapid during infancy and early childhood. Many disease processes impair this development. Therefore, brain developmental age estimation (BDAE) is essential for all diseases affecting cognitive development. Brain…
Segmentation of the developing fetal brain is an important step in quantitative analyses. However, manual segmentation is a very time-consuming task which is prone to error and must be completed by highly specialized indi-viduals.…
Automatic fetal brain tissue segmentation can enhance the quantitative assessment of brain development at this critical stage. Deep learning methods represent the state of the art in medical image segmentation and have also achieved…
Structural magnetic resonance imaging (MRI) has been widely utilized for analysis and diagnosis of brain diseases. Automatic segmentation of brain tumors is a challenging task for computer-aided diagnosis due to low-tissue contrast in the…
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…
Medical image segmentation has become an essential technique in clinical and research-oriented applications. Because manual segmentation methods are tedious, and fully automatic segmentation lacks the flexibility of human intervention or…
Brain age prediction based on children's brain MRI is an important biomarker for brain health and brain development analysis. In this paper, we consider the 3D brain MRI volume as a sequence of 2D images and propose a new framework using…
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…
Accurate automatic segmentation of brain anatomy from $T_1$-weighted~($T_1$-w) magnetic resonance images~(MRI) has been a computationally intensive bottleneck in neuroimaging pipelines, with state-of-the-art results obtained by unsupervised…
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…
Sub-cortical brain structure segmentation in Magnetic Resonance Images (MRI) has attracted the interest of the research community for a long time because morphological changes in these structures are related to different neurodegenerative…
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…
Skull stripping is a common preprocessing step that is often performed manually in Magnetic Resonance Imaging (MRI) pipelines, including functional MRI (fMRI). This manual process is time-consuming and operator dependent. Automating this…
In modern medical diagnostics, magnetic resonance imaging (MRI) is an important technique that provides detailed insights into anatomical structures. In this paper, we present a comprehensive methodology focusing on streamlining the…
Segmenting deep brain structures from magnetic resonance images is important for patient diagnosis, surgical planning, and research. Most current state-of-the-art solutions follow a segmentation-by-registration approach, where subject MRIs…