scholarly journals Collection of Sixteen High-Quality Human Head CAD Models Generated with SimNIBS 2.1 Using Connectome Subject Data within MATLAB® Platform

2018 ◽  
Author(s):  
Aung Thu Htet ◽  
Gregory M. Noetscher ◽  
Edward H. Burnham ◽  
Aapo Nummenmaa ◽  
Sergey N. Makarov
Keyword(s):  
Grey Matter ◽  
Human Head ◽  
Edge Length ◽  
Surface Mesh ◽  
Processing Pipeline ◽  
Software Packages ◽  
Human Connectome Project ◽  
Cad Models ◽  
Mesh Density ◽  
Average Edge Length

AbstractThe goal of this study is to introduce a collection of sixteen high-resolution, 2-manifold CAD compatible head models within the MATLAB platform available to all interested parties for electromagnetic and acoustic simulations. Each model contains skin, skull, CSF, GM, cerebellum, WM, and ventricles head compartments and possesses an “onion” topology: the grey matter shell is a container for white matter, ventricles, and cerebellum objects, the CSF shell contains the grey matter shell, the skull shell contains the CSF shell, and finally the skin or scalp shell contains the skull shell. The models are fully compatible with ANSYS ED FEM software, CST Studio Suite, Sim4Life/SEMCAD software, and other electromagnetic software packages.The collection is based on MRI data from the Human Connectome Project (HCP) segmented using the SimNIBS 2.1/2.1.1 processing pipeline. The average number of triangular surface facets in a model is 866,000, the average triangle quality is 0.25, the average edge length is 1.48 mm, and the average surface mesh density or resolution is 0.57 points per mm2. If necessary, a finer model mesh can be created for every head using available MATLAB tools.

Facile Synthesis of Cu2O Nanocubes in Triblock Copolymer Solutions

2007 ◽  
Vol 121-123 ◽  
pp. 275-278
Author(s):  
Jin Hua Jiang ◽  
Qiu Ming Gao
Keyword(s):  
Triblock Copolymer ◽  
Solar Spectrum ◽  
Blue Shift ◽  
Edge Length ◽  
Promising Candidate ◽  
Organic Species ◽  
Transmission Electron ◽  
Ft Ir ◽  
Average Edge Length

Cuprous oxide and related materials in nanosizes are of much interest and investigated extensively recently. It is reported here that cubic Cu2O nanocubes were synthesized successfully in aqueous solutions at room temperature in air condition. Copper (II) salts in water were reduced with ascorbate acid in air, using the nonionic pluronic amphiphilic triblock copolymer EO20PO70EO20 (P123) as the template-directing and protecting agent. The average edge length of the cubes varied from 50 to 100 nm. Transmission electron microscopy (TEM) has been used for the shape and structural characterization of the obtained Cu2O nanocubes. The UV-Vis spectra showed an obvious blue-shift (0.53 eV), compared to the band gap of the bulk Cu2O crystal, which makes it a promising candidate in solar energy conversion since this sample can make use of higher energy visible rays of solar spectrum. In the FT-IR spectra the peak of Cu-O bond for the Cu2O is clearly distinguished and several weak peaks of the C-H, C-C and C=O bonds for the organic species can also be detectable, implying a little P123 residua in the products. The effect of the triblock copolymer P123 on the growth of the Cu2O nanocubes is discussed.

scholarly journals Using Relion software within Scipion framework

2020 ◽  
Author(s):  
Grigory Sharov ◽  
Dustin R. Morado ◽  
Marta Carroni ◽  
José Miguel de la Rosa-Trevín
Keyword(s):  
Image Processing ◽  
User Interfaces ◽  
Published Data ◽  
New Developments ◽  
Processing Pipeline ◽  
Software Packages ◽  
File Formats ◽  
Processing Framework ◽  
Taking Care

Scipion is a modular image processing framework integrating several software packages under a unified interface while taking care of file formats and conversions. Here new developments and capabilities of the Scipion plugin for the Relion software are presented and illustrated with the image processing pipeline of published data. The user interfaces of Scipion and Relion are compared and the key differences highlighted, allowing this manuscript to be used as a guide for both new and experienced users of these software. Different streaming image processing options are also discussed demonstrating the flexibility of the Scipion framework.SynopsisAn overview of the Scipion plugin for the Relion software is presented and various capabilities of image processing within Scipion framework are discussed.

scholarly journals Inflated false negative rates undermine reproducibility in task-based fMRI

2017 ◽  
Author(s):  
G. Lohmann ◽  
J. Stelzer ◽  
K. Müller ◽  
E. Lacosse ◽  
T. Buschmann ◽  
...  
Keyword(s):  
False Positive ◽  
False Negative ◽  
Sample Sizes ◽  
Test Statistic ◽  
Scientific Validity ◽  
Full Cohort ◽  
Positive Effects ◽  
Software Packages ◽  
Human Connectome Project

AbstractReproducibility is generally regarded as a hallmark of scientific validity. It can be undermined by two very different factors, namely inflated false positive rates or inflated false negative rates. Here we investigate the role of the second factor, i.e. the degree to which true effects are not detected reliably. The availability of large public databases and also supercomputing allows us to tackle this problem quantitatively. Specifically, we estimated the reproducibility in task-based fMRI data over different samples randomly drawn from a large cohort of subjects obtained from the Human Connectome Project. We use the full cohort as a standard of reference to approximate true positive effects, and compute the fraction of those effects that was detected reliably using standard software packages at various smaller sample sizes. We found that with standard sample sizes this fraction was less than 25 percent. We conclude that inflated false negative rates are a major factor that undermine reproducibility. We introduce a new statistical inference algorithm based on a novel test statistic and show that it improves reproducibility without inflating false positive rates.

scholarly journals A fast quadrature-based gravity model for the homogeneous polyhedron

2019 ◽  
Vol 492 (1) ◽  
pp. 420-430
Author(s):  
Jason M Pearl ◽  
Darren L Hitt
Keyword(s):  
Gravitational Field ◽  
Gravity Model ◽  
Approximate Model ◽  
Edge Length ◽  
Gravity Models ◽  
Surface Topology ◽  
Constant Density ◽  
Bulk Properties ◽  
Average Edge Length ◽  
Computationally Expensive

ABSTRACT To date several probes have been sent to explore the Solar system’s asteroids and comets. These bodies are often irregular in shape and to safely navigate probes in their vicinity accurate gravity models are required. For an arbitrarily shaped constant-density body, the gravitational field can be determined from the surface topology and bulk properties. This is achieved by replacing the body’s true geometry with a polyhedron that closely resembles it and for which analytic equations for the gravitational field exist. For some applications however, these equations are too computationally expensive and it can be beneficial to replace them with numerically amenable approximations. In this work, a numerical-quadrature-based model for the gravitational field of a polyhedron consisting of triangular facets is derived. The proposed approximate model is found to be faster than its analytic counterpart. The error of the approximation is found to be negligible for the potential and Laplacian calculations. The approximate model introduces singularities to the surface of the acceleration calculation degrading the solution at altitudes less than the average edge length of the polyhedron.

On average edge length of minimum spanning trees

1999 ◽  
Vol 70 (5) ◽  
pp. 241-243
Author(s):  
Suman Kumar Nath ◽  
Rezaul Alam Chowdhury ◽  
M. Kaykobad
Keyword(s):  
Spanning Trees ◽  
Edge Length ◽  
Minimum Spanning Trees ◽  
Average Edge Length

Reverse Engineering of Mechanical Parts: A Brief Overview of Existing Approaches and Possible New Strategies

2016 ◽  
Author(s):  
Francesco Buonamici ◽  
Monica Carfagni
Keyword(s):  
Reverse Engineering ◽  
A Priori ◽  
Reconstruction Process ◽  
Mechanical Parts ◽  
Cad System ◽  
Software Packages ◽  
Geometrical Constraints ◽  
Cad Models ◽  
Data Points ◽  
New Strategies

Reverse Engineering (RE), also known as “CAD reconstruction”, aims at the reconstruction of 3D geometric models of objects/mechanical parts, starting from 3D measured data (points/mesh). In recent years, considerable developments in RE were achieved thanks to both academic and industrial research (e.g. RE software packages). The aim of this work is to provide an overview of state of the art techniques and approaches presented in recent years (considering at the same time tools and methods provided by commercial CAD software and RE systems). In particular, this article focuses on the “constrained fitting” approach, which considers geometrical constraints between the generated surfaces, improving the reconstruction result. On the basis of the overview, possible theoretical principles are drafted with the aim of suggest new strategies to make the CAD reconstruction process more effective in order to obtain more ready/usable CAD models. Finally, a new RE framework is briefly outlined: the proposed approach hypothesizes a tool built within the environment of an existing CAD system and considers the fitting of a custom-built archetypal model, defined with all the a-priori known dimensions and constraints, to the scanned data.

scholarly journals Improving reproducibility in synchrotron tomography using implementation-adapted filters

2021 ◽  
Vol 28 (5) ◽  
Author(s):  
Poulami Somanya Ganguly ◽  
Daniël M. Pelt ◽  
Doga Gürsoy ◽  
Francesco de Carlo ◽  
K. Joost Batenburg
Keyword(s):  
Reconstruction Algorithm ◽  
Filtered Backprojection ◽  
Computationally Efficient ◽  
Real World Data ◽  
Processing Pipeline ◽  
Software Packages ◽  
Synchrotron Tomography ◽  
Mathematical Formulas ◽  
Computationally Efficient Algorithms ◽  
Tomography Data

For reconstructing large tomographic datasets fast, filtered backprojection-type or Fourier-based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. The continuous mathematical formulas used for image reconstruction in such algorithms are unambiguous. However, variations in discretization and interpolation result in quantitative differences between reconstructed images, and corresponding segmentations, obtained from different software. This hinders reproducibility of experimental results, making it difficult to ensure that results and conclusions from experiments can be reproduced at different facilities or using different software. In this paper, a way to reduce such differences by optimizing the filter used in analytical algorithms is proposed. These filters can be computed using a wrapper routine around a black-box implementation of a reconstruction algorithm, and lead to quantitatively similar reconstructions. Use cases for this approach are demonstrated by computing implementation-adapted filters for several open-source implementations and applying them to simulated phantoms and real-world data acquired at the synchrotron. Our contribution to a reproducible reconstruction step forms a building block towards a fully reproducible synchrotron tomography data processing pipeline.

scholarly journals Sex classification using long-range temporal dependence of resting-state functional MRI time series

2019 ◽  
Author(s):  
Elvisha Dhamala ◽  
Keith W. Jamison ◽  
Mert R. Sabuncu ◽  
Amy Kuceyeski
Keyword(s):  
Sex Differences ◽  
Long Range ◽  
Resting State ◽  
Grey Matter ◽  
Machine Learning Algorithms ◽  
Grey Matter Volume ◽  
Temporal Dependence ◽  
Matter Volume ◽  
Human Connectome Project ◽  
Males And Females

AbstractA thorough understanding of sex differences, if any, that exist in the brains of healthy individuals is crucial for the study of neurological illnesses that exhibit differences in clinical and behavioural phenotypes between males and females. In this work, we evaluate sex differences in regional temporal dependence of resting-state brain activity using 195 male-female pairs (aged 22-37) from the Human Connectome Project. Male-female pairs are strictly matched for total grey matter volume. We find that males have more persistent long-range temporal dependence than females in regions within temporal, parietal, and occipital cortices. Machine learning algorithms trained on regional temporal dependence measures achieve sex classification accuracies of up to 81%. Regions with the strongest feature importance in the sex classification task included cerebellum, amygdala, frontal cortex, and occipital cortex. Additionally, we find that even after males and females are strictly matched on total grey matter volume, significant regional volumetric sex differences persist in many cortical and subcortical regions. Our results indicate males have larger cerebella, hippocampi, parahippocampi, thalami, caudates, and amygdalae while females have larger cingulates, precunei, frontal cortices, and parietal cortices. Sex classification based on regional volume achieves accuracies of up to 85%; cerebellum, cingulate cortex, and temporal cortex are the most important features. These findings highlight the important role of strict volume matching when studying brain-based sex differences. Differential patterns in regional temporal dependence between males and females identifies a potential neurobiological substrate underlying sex differences in functional brain activation patterns and the behaviours with which they correlate.

Modeling of Gelatin-Based Head Phantom Based on its Electrical Properties for Wideband Microwave Imaging Application

2015 ◽  
Vol 781 ◽  
pp. 608-611 ◽  
Author(s):  
Mohd Sollehudin Md Said ◽  
Norhudah Seman ◽  
Noor Redzuan Sulaiman ◽  
Tharek Abd Rahman
Keyword(s):  
Electrical Properties ◽  
Health Monitoring ◽  
Cerebral Spinal Fluid ◽  
Grey Matter ◽  
Imaging System ◽  
Human Head ◽  
Microwave Imaging ◽  
Imaging Application ◽  
Network Analyser ◽  
Investigation And Study

This article presents a human head phantom characterization based on the study of its electrical properties across 1 to 6 GHz. The study focuses on the grey matter, white matter, cerebral spinal fluid (CSF), blood and skin of human head. Through the investigation and study of the human head characteristics, its phantom can be modeled using simple and common materials, which are gelatin, water and sugar. The electrical properties of the chosen mixtures of materials mimicking the electrical properties of human head are measured using special dielectric probe connected to a vector network analyser (VNA). This human head phantom later can be applied in the microwave imaging system for a further study on the health monitoring of human body.

Synthesis of Hollow Ba0.7Sr0.3TiO3 Nanocubes by Using Molten Hydrated Salt as a Solvent

2014 ◽  
Vol 1004-1005 ◽  
pp. 46-50
Author(s):  
Qi An Zhu ◽  
Gao Bai ◽  
Jun Gu Xu ◽  
Jian Xia Wang ◽  
Jin Hui Cai
Keyword(s):  
Phase Composition ◽  
Reaction Time ◽  
Formation Mechanism ◽  
Raw Materials ◽  
Hollow Structure ◽  
Edge Length ◽  
Polycrystalline Structure ◽  
Hydrated Salt ◽  
Phase Pure ◽  
Average Edge Length

Perovskite Ba0.7Sr0.3TiO3nanocubes with a hollow structure were prepared by molten hydrated salt method at 180 °C for 15 h, using Ba (OH)2·8H2O, Sr (OH)2·8H2O and anatase-TiO2as raw materials without any additive or template. The phase composition, morphology and microstructure of the products were characterized by XRD, SEM, TEM and HRTEM. The XRD result indicates that the products are phase pure cubic Ba0.7Sr0.3TiO3, with the calculated unit cella=0.3965 nm. The SEM, TEM and HRTEM results show that the products with polycrystalline structure are composed of the hollow nanocubes whose average edge length is about 180 nm, and their morphologies are greatly influenced by reaction temperature and reaction time. In addition, the formation mechanism of the hollow nanocubes also was discussed.

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