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Outside Publications Referencing PFEIFER

Last updated 7/1/2021

This page contains citations of publications that did not include NRBC personnel but referred to the PFEIFER software.

2021

Md Kafiul Islam, Amir Rastegarnia, and Saeid Sanei. Signal artifacts and techniques for artifacts and noise removal. In Signal Processing Techniques for Computational Health Informatics, pages 23–79. Springer, 2021.

2020

Mengdi Han, Lin Chen, Kedar Aras, Cunman Liang, Xuexian Chen, Hangbo Zhao, Kan Li, Ndeye Rokhaya Faye, Bohan Sun, Jae-Hwan Kim, et al. Catheter-integrated soft multilayer electronic arrays for multiplexed sensing and actuation during cardiac surgery. Nature Biomedical Engineering, 4(10):997– 1009, 2020.

2019

2018

Laura R Bear, Ian J LeGrice, Gregory B Sands, Nigel A Lever, Denis S Loiselle, David J Paterson, Leo K Cheng, and Bruce H Smaill. How accurate is inverse electrocardiographic mapping? a systematic in vivo evaluation. Circulation: Arrhythmia and Electrophysiology, 11(5):e006108, 2018.

Jana Svehlikova, Jan Zelinka, Yesim Serinagaoglu Dogrusoz, Wilson Good, Milan Tysler, and Laura Bear. Impact of signal preprocessing on the inverse localization of the origin of ventricular pacing. In 2018 Computing in Cardiology Conference (CinC), volume 45, pages 1–4. IEEE, 2018.

Shijie Zhou, John L Sapp, Petr &Sbreve;t’ovíček, and B Milan Horáček. Localization of activation origin on patient-specific endocardial surface by the equivalent double layer (edl) source model with sparse bayesian learning. IEEE Transactions on Biomedical Engineering, 66(8):2287–2295, 2018.

2017

Walther HW Schulze, Zhong Chen, Jatin Relan, Danila Potyagaylo, Martin W Krueger, Rashed Karim, Manav Sohal, Anoop Shetty, Ying Liang Ma, Nicholas Ayache, et al. Ecg imaging of ventricular tachycardia: evaluation against simultaneous non-contact mapping and cmr-derived grey zone. Medical & biological engineering & computing, 55(6):979–990, 2017.

Outside Pubs Referencing Cleaver

updated 8/16/2021

This section contains citations of publications that did not include NRBC personnel but referred to the Cleaver software.

2021

João Salinet, Rubén Molero, Fernando S Schlindwein, Jöel Karel, Miguel Rodrigo, José Luis Rojo- Álvarez, Omer Berenfeld, Andreu M Climent, Brian Zenger, Frederique Vanheusden, et al. "Electrocardiographic imaging for atrial fibrillation: a perspective from computer models and animal experiments to clinical value" Frontiers in physiology, 12, 2021.

2020

Julia Boonzaier, Petar I Petrov, Willem M Otte, Nickolay Smirnov, Sebastiaan FW Neggers, and Rick M Dijkhuizen. "Design and evaluation of a rodent-specific transcranial magnetic stimulation coil: An in silico and in vivo validation study." Neuromodulation: Technology at the Neural Interface,23(3):324–334, 2020.

Caroline Mendonca Costa, Caroline Roney, Marina Strocchi, Orod Razeghi, and Steven Niederer. "Clinical translation of patient-specific organ level cardiac models." Modeling and Simulating Cardiac Electrical Activity. Pages 8-1 to 8-19, 2020.

Anh Phong Tran, Shijie Yan, and Qianqian Fang. "Improving model-based functional near-infrared spectroscopy analysis using mesh-based anatomical and light-transport models." Neurophotonics, 7(1):015008, 2020.

Charlotte E Vorwald, Shreeya Joshee, and J Kent Leach. "Spatial localization of endothelial cells in heterotypic spheroids influences notch signaling." Journal of Molecular Medicine, pages 1–11, 2020.

Jing Xu. "Automatic linear and curvilinear mesh generation driven by validity fidelity and topological guarantees." , 2020.

2019

Jiayi Yao, Xiuju Wu, Daoqin Zhang, Lumin Wang, Li Zhang, Eric X Reynolds, Carlos Hernandez, Kristina I Boström, Yucheng Yao, et al. "Elevated endothelial Sox2 causes lumen disruption and cerebral arteriovenous malformations." The Journal of clinical investigation, 129(8):3121–3133, 2019.

2018

Sahar Bakhshian, Zhuofan Shi, Muhammad Sahimi, Theodore T Tsotsis, and Kristian Jessen. "Image-based modeling of gas adsorption and deformation in porous media." Scientific reports, 8(1) pp. 1-12, 2018.

Eloy García, Yago Diez, Oliver Diaz, Xavier Lladó, Robert Martý, Joan Martý, and Arnau Oliver. "A step-by-step review on patient-specific biomechanical finite element models for breast mri to x-ray mammography registration." Medical physics, 45(1):e6–e31, 2018.

Ho Quang Nguyen, Tien Tuan Dao, Alain Rassineux, and Marie Christine Ho Ba Tho. "Material-driven mesh of the lumbar spine derived from CT data." Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 6(2):128–136, 2018.

Jared Vicory, Ethan Murphy, and Ryan J Halter. "Creation and visualization of high-quality tetrahedral meshes from segmentations using 3d slicer." ELECTRICAL IMPEDANCE TOMOGRAPHY, page 55, 2018.

2017

Mar Cortes, Laura Dubreuil Vall, Giulio Ruffini, Douglas Labar, and Dylan Edwards. "Transcranial direct current stimulation in chronic spinal cord injury: quantitative eeg study." Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation 10(1):e13, 2017.

Fotios Drakopoulos. "Finite Element Modeling Driven by Health Care and Aerospace Applications." PhD thesis, Old Dominion University, 2017.

Jacob Fish and Nan Hu. "Multiscale modeling of femur fracture." International Journal for Numerical Methods in Engineering, 111(1):3–25, 2017.

Kathleen M Friel, Peter Lee, Disha Gupta, Hsing-Ching Kuo, Ana RP Smorenburg, and Dylan J Edwards. "Combined transcranial direct current stimulation and upper extremity robotic therapy improves upper extremity function in an adult with cerebral palsy: A pilot study." Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 10(1):e13, 2017.

Anh Phong Tran and Qianqian Fang. "Fast and high-quality tetrahedral mesh generation from neuroanatomical scans." arXiv preprint, arXiv:1708.08954, 2017.

Laura Dubreuil Vall, Mar Cortes, Dylan Edwards, Giulio Ruffini, and David Putrino. "EEG recordings during sham control transcranial direct current stimulation protocol." Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 10(1):e13, 2017.

Chuan Wang, Jie Zhu, Yanwen Guo, and Wenping Wang. "Video vectorization via tetrahedral remeshing." IEEE Transactions on Image Processing, 26(4):1833–1844, 2017.

Jing Xu and Andrey N Chernikov. "Homeomorphic tetrahedralization of multi-material images with quality and fidelity guarantees." Procedia engineering, 203:40–52, 2017.

2016

Yu Andy Huang. Computational Models of Current Flow in Transcranial Electrical Stimulation. PhD thesis, The City College of New York, 2016.

Kepler Status

Tesla Status

Software Release System Documentation

Software File Naming Policy

Software releases are served from the Qumulo server under /releases/... The mount is \\qumulo\releases. If you will be releasing software contact IT to get access to this server. The download tracking system parses the log files to gather data about downloads of our software. The system parses the names of the directories and files within to determine what products and versions were downloaded. It may also use an XML file included with the release to gather data about the files. The version number from release folders are also used to determine which release is most recent and therefore which one should be presented to users for download by default. It is important for the naming convention and standards to be followed in order for the system to work properly.

Major releases should placed in a folder named starting with the name of the software. Capitalization should be consistent with previous releases. The name should be followed by an underscore, then 'v' followed by the release number. The version number shall consist of only numbers and '.' characters. The number may also include a, b, c, etc. at the end, but this should not be needed since build numbers can be used within major releases.

Examples:

map3d_v6.5

seg3d_v1.9.4

scirun_v4.0

Within major release folders, files should be named starting with the name of the software or item. Capitalization should be consistent across files. The name should be followed by an underscore character then the major version number if used. If a sub-build number is used, an underscore character should seperate it from the major build number. The sub-build number shall be based on the date, 8 numbers - YYYYMMDD, i.e. 20080712. An underscore character should be used to seperate OS and platform info from the version or sub-build number. A dash caracter '-' should be used to seperate OS from platform info. Capitalization should be consistent across files. This should be followed by the file extension in lower case.

No sub folders should be used within the major release folder.

Examples:

Seg3D_1.9.4_Intel.dmg

Seg3D_1.9.4_Linux-x86-64.tar.gz

Seg3D_1.9.4_Win32-installer.exe

Seg3D_1.9.4_Ubuntu0-amd64.deb

AA-Paw.nrrd

With Build Numbers:

SCIRun_4.0_20080324_Darwin-Intel32.dmg

SCIRun_4.0_20080717_WinXP.exe

SCIRun_4.0_20080324_Darwin-PPC32.dmg

SCIRunData_20080717.zip

XML File

An xml file may also be included to provide data about the files. It should be named "fileinfo.xml". If detected, this will be used in preference to parsing the file names. Therefore, if an XML file is used it is not strictly necessary to follow the naming convention. Similar guidelines should be followed as far as labeling consistency from release to release. The example below can be used as a template. Content within the "<note>" tags will be displayed as bullet items listed in the right column. Content in "<warning>" tags will be similarly displayed but in red. The parent build tag can contain URL parameters for links to release notes documents and the home URL for the software. Whenever possible it is best to use the registered domain name for the software homeURL because it will always resolve to the right place no matter what changes to the final page URL occur in the future.

<?xml version="1.0" encoding="UTF-8" ?>
<build releasedate="January 1, 2011" releasenotesURL="http://www.sci.utah.edu/releases/mysoftware_v1.3.5/ReleaseNotes.txt"
homeURL="http://www.mysoftware.org">
    <note>See product documentation for details on new features and how to use it.</note>
    <file name="MySoftware_1.3.5_win32.zip" product="MySoftware" ver="1.3.5" distribution="Windows 32bit">
        <note>MySoftware 1.3.5 32bit Windows</note>
        <warning>This will not work on a Mac</warning>
    </file>
    <file name="MySoftware_1.3.5_win64.exe" product="MySoftware" ver="1.3.5" distribution="Windows 64bit" />
    <file name="MySoftware_1.3.5_Darwin.dmg" product="MySoftware" ver="1.3.5" distribution="Darwin OSX" />
    <file name="MySoftware_1.3.5_source.zip" product="MySoftware" ver="1.3.5" distribution="Source" />
    <file name="data.zip" product="MySoftware Data" ver="1.3.5" distribution="All" />
</build>

File Permissions

In order for the web server to be able to access the release files, they should at least have group and world read access (in numeric terms, 644; -rw-r--r-- as seen by ls -l ), with the directory for the release having group and world read and execute permissions (in numeric terms, 755; -rwxr-xr-x as seen by ls -l). Problems with permission setting may cause the download page to be blank or cause an error when users click on the links to download. Always verify that downloading works for each file! IT (This email address is being protected from spambots. You need JavaScript enabled to view it.) can help if you have any problem setting permissions.