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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…

Fetal brain extraction is a necessary first step in most computational fetal brain MRI pipelines. However, it has been a very challenging task due to non-standard fetal head pose, fetal movements during examination, and vastly heterogeneous…

Brain extraction in magnetic resonance imaging (MRI) data is an important segmentation step in many neuroimaging preprocessing pipelines. Image segmentation is one of the research fields in which deep learning had the biggest impact in…

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…

Skull stripping magnetic resonance images (MRI) of the human brain is an important process in many image processing techniques, such as automatic segmentation of brain structures. Numerous methods have been developed to perform this task,…

Brain extraction is a fundamental step for most brain imaging studies. In this paper, we investigate the problem of skull stripping and propose complementary segmentation networks (CompNets) to accurately extract the brain from T1-weighted…

Brain extraction (skull stripping) is a challenging problem in neuroimaging. It is due to the variability in conditions from data acquisition or abnormalities in images, making brain morphology and intensity characteristics changeable and…

Brain extraction is a critical preprocessing step in the analysis of MRI neuroimaging studies and influences the accuracy of downstream analyses. The majority of brain extraction algorithms are, however, optimized for processing healthy…

Prediction of the cognitive evolution of a person susceptible to develop a neurodegenerative disorder is crucial to provide an appropriate treatment as soon as possible. In this paper we propose a 3D siamese network designed to extract…

Whole brain extraction, also known as skull stripping, is a process in neuroimaging in which non-brain tissue such as skull, eyeballs, skin, etc. are removed from neuroimages. Skull striping is a preliminary step in presurgical planning,…

To improve the performance of most neuroimiage analysis pipelines, brain extraction is used as a fundamental first step in the image processing. But in the case of fetal brain development, there is a need for a reliable US-specific tool. In…

Many functional and structural neuroimaging studies call for accurate morphometric segmentation of different brain structures starting from image intensity values of MRI scans. Current automatic (multi-) atlas-based segmentation strategies…

Brain extraction from images is a common pre-processing step. Many approaches exist, but they are frequently only designed to perform brain extraction from images without strong pathologies. Extracting the brain from images with strong…

MR images of fetuses allow clinicians to detect brain abnormalities in an early stage of development. The cornerstone of volumetric and morphologic analysis in fetal MRI is segmentation of the fetal brain into different tissue classes.…

This paper investigates the numerical uncertainty of Convolutional Neural Networks (CNNs) inference for structural brain MRI analysis. It applies Random Rounding -- a stochastic arithmetic technique -- to CNN models employed in non-linear…

Automated fetal brain extraction from full-uterus MRI is a challenging task due to variable head sizes, orientations, complex anatomy, and prevalent artifacts. While deep-learning (DL) models trained on synthetic images have been successful…

Convolutional neural networks (CNN) for medical imaging are constrained by the number of annotated data required in the training stage. Usually, manual annotation is considered to be the "gold standard". However, medical imaging datasets…

The willingness to trust predictions formulated by automatic algorithms is key in a vast number of domains. However, a vast number of deep architectures are only able to formulate predictions without an associated uncertainty. In this…

In this work, we investigate the value of uncertainty modeling in 3D super-resolution with convolutional neural networks (CNNs). Deep learning has shown success in a plethora of medical image transformation problems, such as…

Rodent stroke models are important for evaluating treatments and understanding the pathophysiology and behavioral changes of brain ischemia, and magnetic resonance imaging (MRI) is a valuable tool for measuring outcome in preclinical…