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simBio specifications

Information


Unique identifier OMICS_29789
Name simBio
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU Lesser General Public License version 3.0
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes

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Publication for simBio

simBio citations

 (7)
library_books

The FieldTrip SimBio pipeline for EEG forward solutions

2018
Biomed Eng Online
PMCID: 5870695
PMID: 29580236
DOI: 10.1186/s12938-018-0463-y

[…] As the first step to generate segmentations in the FieldTrip-SimBio pipeline, the SPM toolbox is used to compute masks of gray matter, white matter, and CSF based on a T1-MRI. A rough skull segmentation is created by dilating the union of these three masks, and […]

library_books

Detecting Large Scale Brain Networks Using EEG: Impact of Electrode Density, Head Modeling and Source Localization

2018
Front Neuroinform
PMCID: 5841019
PMID: 29551969
DOI: 10.3389/fninf.2018.00004

[…] ing the Iterative Closest Point registration algorithm () implemented in SPM12. After associating each tissue class with a representative conductivity value () (see Supplementary Table ), we used the SimBio finite element method (FEM) integrated in FieldTrip for the numerical approximation of the volume conduction model (). Alternatively to the SimBio-FEM, a boundary element method (BEM) solution […]

library_books

The Discontinuous Galerkin Finite Element Method for Solving the MEG and the Combined MEG/EEG Forward Problem

2018
Front Neurosci
PMCID: 5801436
PMID: 29456487
DOI: 10.3389/fnins.2018.00030

[…] esolution meshes especially in the source area, a result which is in line with ours. Deeper comparisons are again not easy because of different set-ups, but we are planning a direct comparison of the SimBio code used by Vorwerk () and our DUNEuro implementation in future studies.In Vorwerk et al. (), a guideline for EEG and MEG forward modeling using CG-FEM Saint Venant modeling was presented in r […]

call_split

Zoomed MRI Guided by Combined EEG/MEG Source Analysis: A Multimodal Approach for Optimizing Presurgical Epilepsy Work up and its Application in a Multi focal Epilepsy Patient Case Study

2017
PMCID: 5495874
PMID: 28510905
DOI: 10.1007/s10548-017-0568-9
call_split See protocol

[…] (0.43) (Ramon et al. ), CSF (1.79) (Baumann et al. ), GM (0.33) (Fuchs et al. ), dura mater (0.1) (Ramon ).A geometry adapted hexahedral finite element mesh was created out of the segmented MRI using SimBio-VGRID. Geometry adapted hexahedral meshes provide a good balance by achieving better conformance to the geometry than regular hexahedral meshes whilst being less time-consuming and complicated […]

library_books

Electrical Stimulation of the Human Cerebral Cortex by Extracranial Muscle Activity: Effect Quantification With Intracranial EEG and FEM Simulations

2016
IEEE Trans Biomed Eng
PMCID: 5298223
PMID: 27448334
DOI: 10.1109/TBME.2016.2570743

[…] FEM forward calculations were computed with SimBio [] using the St. Venant dipole modeling approach [], []. The conductivity values used were derived from the resistivity values used in [], namely white matter 0.14 S/m, gray matter 0.33 S/m, CS […]

library_books

The role of blood vessels in high resolution volume conductor head modeling of EEG

2015
Neuroimage
PMCID: 5225375
PMID: 26747748
DOI: 10.1016/j.neuroimage.2015.12.041

[…] FEM forward calculations were computed with SimBio-NeuroFEM () using the Saint-Venant direct approach (; ; ) based on geometry-adapted cubic meshes () (cf. for details), which improve the precision of the computed potentials by reducing the er […]

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simBio institution(s)
Department of Physiology and Biophysics, Kyoto University Graduate School of Medicine, Kyoto, Japan
simBio funding source(s)
Supported by the program for promotion of fundamental studies in health sciences of the organization for pharmaceutical safety and research, a grant-in-aid for scientific research, and the leading project for biosimulation from the Japanese Ministry of Education, culture, sports, science and technology.

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