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Brain segmentation

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https://www.readbyqxmd.com/read/28227989/computational-models-of-non-invasive-brain-and-spinal-cord-stimulation
#1
Pedro C Miranda, Ricardo Salvador, Cornelia Wenger, Sofia R Fernandes, Pedro C Miranda, Ricardo Salvador, Cornelia Wenger, Sofia R Fernandes, Sofia R Fernandes, Pedro C Miranda, Cornelia Wenger, Ricardo Salvador
Non-invasive brain and spinal cord stimulation techniques are increasingly used for diagnostic and therapeutic purposes. Knowledge of the spatial distribution of the induced electric field is necessary to interpret experimental results and to optimize field delivery. Since the induced electric field cannot be measured in vivo in humans, computational models play a fundamental role in determining the characteristics of the electric field. We produced computational models of the head and trunk to calculate the electric field induced in the brain and spinal cord by transcranial magnetic stimulation, transcranial direct current stimulation and transcutaneous spinal cord direct current stimulation...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227960/automated-volumetry-for-unilateral-hippocampal-sclerosis-detection-in-patients-with-temporal-lobe-epilepsy
#2
Cristina Martins, Nadia Moreira da Silva, Guilherme Silva, Verena E Rozanski, Joao Paulo Silva Cunha, Cristina Martins, Nadia Moreira da Silva, Guilherme Silva, Verena E Rozanski, Joao Paulo Silva Cunha, Joao Paulo Silva Cunha, Guilherme Silva, Verena E Rozanski, Nadia Moreira da Silva, Cristina Martins
Hippocampal sclerosis (HS) is the most common cause of temporal lobe epilepsy (TLE) and can be identified in magnetic resonance imaging as hippocampal atrophy and subsequent volume loss. Detecting this kind of abnormalities through simple radiological assessment could be difficult, even for experienced radiologists. For that reason, hippocampal volumetry is generally used to support this kind of diagnosis. Manual volumetry is the traditional approach but it is time consuming and requires the physician to be familiar with neuroimaging software tools...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227881/a-framework-for-informing-segmentation-of-in-vivo-mri-with-information-derived-from-ex-vivo-imaging-application-in-the-medial-temporal-lobe
#3
Paul A Yushkevich, Laura Wisse, Daniel Adler, Ranjit Ittyerah, John B Pluta, John L Robinson, Theresa Schuck, John Q Trojanowski, Murray Grossman, John A Detre, Mark A Elliott, Jon B Toledo, Weixia Liu, Stephen Pickup, Sandhitsu R Das, David A Wolk, Paul A Yushkevich, Laura Wisse, Daniel Adler, Ranjit Ittyerah, John B Pluta, John L Robinson, Theresa Schuck, John Q Trojanowski, Murray Grossman, John A Detre, Mark A Elliott, Jon B Toledo, Weixia Liu, Stephen Pickup, Sandhitsu R Das, David A Wolk, John L Robinson, Jon B Toledo, Stephen Pickup, Weixia Liu, Paul A Yushkevich, Daniel Adler, John Q Trojanowski, Theresa Schuck, David A Wolk, Laura Wisse, Mark A Elliott, Sandhitsu R Das, John A Detre, John B Pluta, Ranjit Ittyerah, Murray Grossman
Automatic segmentation of cortical and subcortical structures is commonplace in brain MRI literature and is frequently used as the first step towards quantitative analysis of structural and functional neuroimaging. Most approaches to brain structure segmentation are based on propagation of anatomical information from example MRI datasets, called atlases or templates, that are manually labeled by experts. The accuracy of automatic segmentation is usually validated against the "bronze" standard of manual segmentation of test MRI datasets...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227867/knife-edge-scanning-microscopy-for-in-silico-study-of-cerebral-blood-flow-from-biological-imaging-data-to-flow-simulations
#4
Michael R Nowak, Alexander Lozovskiy, Dimitri Dobroskok, Yoonsuck Choe, Michael R Nowak, Alexander Lozovskiy, Dimitri Dobroskok, Yoonsuck Choe, Dimitri Dobroskok, Michael R Nowak, Alexander Lozovskiy, Yoonsuck Choe
Knife-edge scanning microscopy provides the capability to image whole-brain cerebral microvasculature of small organisms, such as mice, at sub-micron resolution, providing a feasible foundation for the reconstruction of circulatory pathways from the systemic to cellular scale. In this paper, we illustrate the feasibility of using this data to model cerebral blood flow using numerical simulations. Starting with a small vascular element in microcirculation of interest, we present its segmentation from the imaging-data volume, construction of its triangular surface mesh, assembly of its tetrahedral volumetric mesh from the surface, and then conclude with Stokes flow simulation of plasma through the microvascular vessel...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227864/automatic-segmentation-of-multimodal-brain-tumor-images-based-on-classification-of-super-voxels
#5
M Kadkhodaei, S Samavi, N Karimi, H Mohaghegh, S M R Soroushmehr, K Ward, A All, K Najarian, M Kadkhodaei, S Samavi, N Karimi, H Mohaghegh, S M R Soroushmehr, K Ward, A All, K Najarian, K Ward, S M R Soroushmehr, A All, S Samavi, M Kadkhodaei, H Mohaghegh, K Najarian, N Karimi
Despite the rapid growth in brain tumor segmentation approaches, there are still many challenges in this field. Automatic segmentation of brain images has a critical role in decreasing the burden of manual labeling and increasing robustness of brain tumor diagnosis. We consider segmentation of glioma tumors, which have a wide variation in size, shape and appearance properties. In this paper images are enhanced and normalized to same scale in a preprocessing step. The enhanced images are then segmented based on their intensities using 3D super-voxels...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227795/simplified-realistic-human-head-model-for-simulating-tumor-treating-fields-ttfields
#6
Cornelia Wenger, Ze'ev Bomzon, Ricardo Salvador, Peter J Basser, Pedro C Miranda, Cornelia Wenger, Ze'ev Bomzon, Ricardo Salvador, Peter J Basser, Pedro C Miranda, Peter J Basser, Pedro C Miranda, Cornelia Wenger, Ricardo Salvador, Ze'ev Bomzon
Tumor Treating Fields (TTFields) are alternating electric fields in the intermediate frequency range (100-300 kHz) of low-intensity (1-3 V/cm). TTFields are an anti-mitotic treatment against solid tumors, which are approved for Glioblastoma Multiforme (GBM) patients. These electric fields are induced non-invasively by transducer arrays placed directly on the patient's scalp. Cell culture experiments showed that treatment efficacy is dependent on the induced field intensity. In clinical practice, a software called NovoTal(TM) uses head measurements to estimate the optimal array placement to maximize the electric field delivery to the tumor...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227766/short-association-bundle-atlas-based-on-inter-subject-clustering-from-hardi-data
#7
C Roman, M Guevara, D Duclap, A Lebois, C Poupon, J-F Mangin, P Guevara, C Roman, M Guevara, D Duclap, A Lebois, C Poupon, J-F Mangin, P Guevara, J-F Mangin, C Roman, D Duclap, C Poupon, A Lebois, P Guevara, M Guevara
This paper is focused on the study of short brain association fibers. We present an automatic method to identify short bundles of the superficial white matter based on inter-subject hierarchical clustering. Our method finds clusters of similar fibers, belonging to the different subjects, according to a distance measure between fibers. First, the algorithm obtains representative bundles and subsequently we perform an automatic labeling based on the anatomy, of the most stable connections. The analysis was applied to two independent groups of 37 subjects...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227405/template-based-rodent-brain-extraction-and-atlas-mapping
#8
Weimin Huang, Jiaqi Zhang, Zhiping Lin, Su Huang, Yuping Duan, Zhongkang Lu, Weimin Huang, Jiaqi Zhang, Zhiping Lin, Su Huang, Yuping Duan, Zhongkang Lu, Jiaqi Zhang, Weimin Huang, Yuping Duan, Zhongkang Lu, Zhiping Lin, Su Huang
Accurate rodent brain extraction is the basic step for many translational studies using MR imaging. This paper presents a template based approach with multi-expert refinement to automatic rodent brain extraction. We first build the brain appearance model based on the learning exemplars. Together with the template matching, we encode the rodent brain position into the search space to reliably locate the rodent brain and estimate the rough segmentation. With the initial mask, a level-set segmentation and a mask-based template learning are implemented further to the brain region...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227404/evaluation-of-the-effect-of-doubling-atlases-using-midsagittal-plane-on-multi-atlas-based-segmentation-of-brain-structures
#9
Subrahmanyam Gorthi, Subrahmanyam Gorthi, Subrahmanyam Gorthi
Normal human brain exhibits approximately bi-fold symmetry with respect to its midsagittal plane (MSP). The objective of this work is to investigate the effect of doubling atlases (i.e., reference images) used in multi-atlas fusion methods by exploiting the inherent bilateral symmetry of human brain. To this end, we perform automated segmentation of 15 subcortical structures using Local Weighted Voting (LWV) fusion method with varying number of atlases. We consider three specific scenarios for atlases while performing fusion: (i) fusion with original OASIS atlases, (ii) with atlases obtained by flipping the original atlases based on their MSP, and (iii) with both original and flipped atlases...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227388/learning-to-distinguish-cerebral-vasculature-data-from-mechanical-chatter-in-india-ink-images-acquired-using-knife-edge-scanning-microscopy
#10
Michael R Nowak, Yoonsuck Choe, Michael R Nowak, Yoonsuck Choe, Michael R Nowak, Yoonsuck Choe
We introduce a simple, yet effective, procedure for accurate classification of connected components embedded in biological images. In our method, a training set is generated from user-delineated features of manually-labeled examples; we subsequently train a classifier using the resultant training set. The overall process is described using imaging data acquired from an India-ink perfused C57BL/6J mouse brain using Knife Edge Scanning Microscopy. We illustrate the procedure through segmentation of cerebral vasculature structures from mechanical noise using trained classifiers...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227104/source-and-sink-nodes-in-absence-seizures
#11
Abner C Rodrigues, Birajara S Machado, Luis Otavio S F Caboclo, Andre Fujita, Luiz A Baccaia, Koichi Sameshima, Abner C Rodrigues, Birajara S Machado, Luis Otavio S F Caboclo, Andre Fujita, Luiz A Baccala, Koichi Sameshima, Luiz A Baccala, Biraiara S Machado, Luis Otavio S F Caboclo
As opposed to focal epilepsy, absence seizures do not exhibit a clear seizure onset zone or focus since its ictal activity rapidly engages both brain hemispheres. Yet recent graph theoretical analysis applied to absence seizures EEG suggests the cortical focal presence, an unexpected feature for this type of epilepsy. In this study, we explore the characteristics of absence seizure by classifying the nodes as to their source/sink natures via weighted directed graph analysis based on connectivity direction and strength estimation using information partial directed coherence (iPDC)...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226725/a-chicken-embryo-cardiac-outflow-tract-atlas-for-registering-changes-due-to-abnormal-blood-flow
#12
James P Carson, Monique Y Rennie, Michael Danilchik, Kent Thornburg, Sandra Rugonyi, James P Carson, Monique Y Rennie, Michael Danilchik, Kent Thornburg, Sandra Rugonyi, Kent Thornburg, Michael Danilchik, James P Carson, Monique Y Rennie, Sandra Rugonyi
Subdivision-based image registration has previously been applied to co-localize digital information extracted from rigid structures in biological specimens, such as the brain. Here, we describe and demonstrate the creation and application of a two-dimensional subdivision-based atlas representing a dynamic structure: the outflow tract of the developing chicken heart. The atlas is designed to segment three different anatomical layers of the outflow tract, and is demonstrated on the characterization of collagen XIV in both control and induced abnormal flow specimens...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226695/creation-of-a-whole-brain-short-association-bundle-atlas-using-a-hybrid-approach
#13
M Guevara, C Roman, J Houenou, D Duclap, C Poupon, J-F Mangin, P Guevara, M Guevara, C Roman, J Houenou, D Duclap, C Poupon, J-F Mangin, P Guevara, J-F Mangin, C Roman, D Duclap, C Poupon, J Houenou, P Guevara, M Guevara
The Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of pathogenesis triggered by abnormal connectivity. In this work we expanded a previously developed method for the automatic creation of a whole brain SWM bundle atlas. The method is based on a hybrid approach. First a cortical parcellation is used to extract fibers connecting two regions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226446/a-challenging-issue-detection-of-white-matter-hyperintensities-in-neonatal-brain-mri
#14
Baptiste Morel, Yongchao Xu, Alessio Virzi, Thierry Geraud, Catherine Adamsbaum, Isabelle Bloch, Baptiste Morel, Yongchao Xu, Alessio Virzi, Thierry Geraud, Catherine Adamsbaum, Isabelle Bloch, Alessio Virzi, Yongchao Xu, Thierry Geraud, Catherine Adamsbaum, Isabelle Bloch, Baptiste Morel
The progress of magnetic resonance imaging (MRI) allows for a precise exploration of the brain of premature infants at term equivalent age. The so-called DEHSI (diffuse excessive high signal intensity) of the white matter of premature brains remains a challenging issue in terms of definition, and thus of interpretation. We propose a semi-automatic detection and quantification method of white matter hyperintensities in MRI relying on morphological operators and max-tree representations, which constitutes a powerful tool to help radiologists to improve their interpretation...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225689/sex-differences-in-anthropometrics-and-heading-kinematics-among-division-i-soccer-athletes
#15
Abigail C Bretzin, Jamie L Mansell, Ryan T Tierney, Jane K McDevitt
BACKGROUND: Soccer players head the ball repetitively throughout their careers; this is also a potential mechanism for a concussion. Although not all soccer headers result in a concussion, these subconcussive impacts may impart acceleration, deceleration, and rotational forces on the brain, leaving structural and functional deficits. Stronger neck musculature may reduce head-neck segment kinematics. HYPOTHESIS: The relationship between anthropometrics and soccer heading kinematics will not differ between sexes...
March 2017: Sports Health
https://www.readbyqxmd.com/read/28224379/nerves-of-steel-a-low-cost-method-for-3d-printing-the-cranial-nerves
#16
Ramin Javan, Duncan Davidson, Afshin Javan
Steady-state free precession (SSFP) magnetic resonance imaging (MRI) can demonstrate details down to the cranial nerve (CN) level. High-resolution three-dimensional (3D) visualization can now quickly be performed at the workstation. However, we are still limited by visualization on flat screens. The emerging technologies in rapid prototyping or 3D printing overcome this limitation. It comprises a variety of automated manufacturing techniques, which use virtual 3D data sets to fabricate solid forms in a layer-by-layer technique...
February 21, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28223187/deepnat-deep-convolutional-neural-network-for-segmenting-neuroanatomy
#17
Christian Wachinger, Martin Reuter, Tassilo Klein
We introduce DeepNAT, a 3D Deep convolutional neural network for the automatic segmentation of NeuroAnaTomy in T1-weighted magnetic resonance images. DeepNAT is an end-to-end learning-based approach to brain segmentation that jointly learns an abstract feature representation and a multi-class classification. We propose a 3D patch-based approach, where we do not only predict the center voxel of the patch but also neighbors, which is formulated as multi-task learning. To address a class imbalance problem, we arrange two networks hierarchically, where the first one separates foreground from background, and the second one identifies 25 brain structures on the foreground...
February 18, 2017: NeuroImage
https://www.readbyqxmd.com/read/28220987/brain-tissue-reaction-to-deep-brain-stimulation-a-longitudinal-study-of-dbs-in-the-goettingen-minipig
#18
Dariusz Orlowski, Alexandre Michalis, Andreas N Glud, Anders R Korshøj, Lise M Fitting, Trine W Mikkelsen, André Mercanzini, Alain Jordan, Alain Dransart, Jens C H Sørensen
OBJECTIVES: The use of Deep Brain Stimulation (DBS) in treatment of various brain disorders is constantly growing; however, the number of studies of the reaction of the brain tissue toward implanted leads is still limited. Therefore, the aim of our study was to analyze the impact of DBS leads on brain tissue in a large animal model using minipigs. METHODS: Twelve female animals, one control and eleven with bilaterally implanted DBS electrodes were used in our experiment...
February 21, 2017: Neuromodulation: Journal of the International Neuromodulation Society
https://www.readbyqxmd.com/read/28220142/absence-of-an-n-linked-glycosylation-motif-in-the-glycoprotein-of-the-live-attenuated-argentine-hemorrhagic-fever-vaccine-candid-1-results-in-its-improper-processing-and-reduced-surface-expression
#19
John T Manning, Alexey V Seregin, Nadezhda E Yun, Takaaki Koma, Cheng Huang, José Barral, Juan C de la Torre, Slobodan Paessler
Junin virus (JUNV), a highly pathogenic New World arenavirus, is the causative agent of Argentine hemorrhagic fever (AHF). The live-attenuated Candid #1 (Can) strain currently serves as a vaccine for at-risk populations. We have previously shown that the Can glycoprotein (GPC) gene is the primary gene responsible for attenuation in a guinea pig model of AHF. However, the mechanisms through which the GPC contributes to the attenuation of the Can strain remain unknown. A more complete understanding of the mechanisms underlying the attenuation and immunogenicity of the Can strain will potentially allow for the rational design of additional safe and novel vaccines...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28219833/statistical-appearance-models-based-on-probabilistic-correspondences
#20
Julia Krüger, Jan Ehrhardt, Heinz Handels
Model-based image analysis is indispensable in medical image processing. One key aspect of building statistical shape and appearance models is the determination of one-to-one correspondences in the training data set. At the same time, the identification of these correspondences is the most challenging part of such methods. In our earlier work, we developed an alternative method using correspondence probabilities instead of exact one-to-one correspondences for a statistical shape model (Hufnagel et al., 2008)...
February 7, 2017: Medical Image Analysis
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