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Zeffiro Forward and Inverse Interface for Complex Geometries

version 5.1.1 (107 MB) by Sampsa Pursiainen
Simple tool for finite element based forward and inverse simulations in complex geometries

381 Downloads

Updated 24 Mar 2022

From GitHub

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Zeffiro Interface (ZI), © 2018- Sampsa Pursiainen & ZI Development Team, is an open source code package constituting an accessible tool for multidisciplinary finite element method (FEM) assisted forward and inverse simulations in complex geometries.
With ZI, one can segment a realistic multilayer geometry and generate a multi-compartment FE mesh, if triangular ASCII surface grids (in DAT or ASC file format) are available. A suitable surface segmentation can be produced, for example, with the FreeSurfer software suite (Copyright © FreeSurfer, 2013). Such a segmentation can be imported at once from a folder containing a set of ASCII files. An example folder can be found in the repository. ZI allows also importing a parcellation created with FreeSurfer to enable distinguishing different brain regions and, thereby, analysing the connectivity of the brain function over a time series. Different compartments can be defined as active, allowing the analysis of the sub-cortical strucures. In each compartment, the orientation of the activity can be either normally constrained or unconstrained. The main routines of ZI can be accelerated significantly in a computer equipped with a graphics computing unit (GPU). It is especially recommendable to perform the forward simulation process, i.e., to generate the finite element mesh, the lead field matrix and to interpolate between different point sets, utilizing a GPU. After the forward simulation phase, the model can be processed also without GPU acceleration.
A brief introduction to the essential features of the interface can be found at:
The interface itself has been introduced in:
He, Q., Rezaei, A. & Pursiainen, S. (2019). Zeffiro User Interface for Electromagnetic Brain Imaging: a GPU Accelerated FEM Tool for Forward and Inverse Computations in Matlab. Neuroinformatics, doi:10.1007/s12021-019-09436-9
The essential mathematical techniques used in the interface have been reviewed and validated in:
Miinalainen, T., Rezaei, A., Us, D., Nüßing, A., Engwer, C., Wolters, C. H., & Pursiainen, S. (2019). A realistic, accurate and fast source modeling approach for the EEG forward problem. NeuroImage, 184, 56-67.
Pursiainen, S. (2012). Raviart–Thomas-type sources adapted to applied EEG and MEG: implementation and results. Inverse Problems, 28(6), 065013.
The IAS MAP (iterative alternating sequential maximum a posteriori) inversion method and the hierarchical Bayesian sampler are based on:
Calvetti, D., Hakula, H., Pursiainen, S., & Somersalo, E. (2009). Conditionally Gaussian hypermodels for cerebral source localization. SIAM Journal on Imaging Sciences, 2(3), 879-909.
It has been applied for a realistic brain geometry, e.g., in:
Lucka, F., Pursiainen, S., Burger, M., & Wolters, C. H. (2012). Hierarchical Bayesian inference for the EEG inverse problem using realistic FE head models: depth localization and source separation for focal primary currents. Neuroimage, 61(4), 1364-1382.
The current preserving source model combines linear (face-intersecting) and quadratic (edgewise) elements via the Position Based Optimization (PBO) method and the 10-source stencil in which 4 face sources and 6 edge sources are applied for each tetrahedral element containing a source:
Bauer, M., Pursiainen, S., Vorwerk, J., Köstler, H., & Wolters, C. H. (2015). Comparison study for Whitney (Raviart–Thomas)-type source models in finite-element-method-based EEG forward modeling. IEEE Transactions on Biomedical Engineering, 62(11), 2648-2656.
Pursiainen, S., Vorwerk, J., & Wolters, C. H. (2016). Electroencephalography (EEG) forward modeling via H (div) finite element sources with focal interpolation. Physics in Medicine & Biology, 61(24), 8502.
ZI is not designed to be used in clinical applications. The authors do not take the responsibility of the results obtained with ZI using clinical data.

Cite As

Sampsa Pursiainen (2022). Zeffiro Forward and Inverse Interface for Complex Geometries (https://github.com/sampsapursiainen/zeffiro_interface), GitHub. Retrieved .

MATLAB Release Compatibility
Created with R2018a
Compatible with R2013a to R2018a
Platform Compatibility
Windows macOS Linux

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cluster/csc

cluster/csc/IntegrationScripts/puhti

cluster/example

m

m/auxiliary_scripts

m/auxiliary_scripts/analysisScripts

m/auxiliary_scripts/mesh_averaging

m/auxiliary_scripts/mri

m/constants

m/forward_scripts/brain

m/forward_scripts/general

m/forward_scripts/gravity

m/graph_bank

m/inverse_data_processing

m/operators

m/time_series_tools

mlapp

plugins/Beamformer

plugins/ClassicalSparseMethods

plugins/CreateDipolarPair/m

plugins/DipoleScan

plugins/DipoleScan/m

plugins/DynamicalPlotQueue/m

plugins/DynamicalPlotQueue/m/dynamical_plot_queue_bank

plugins/EITSensitivityTool/m

plugins/EXP/common

plugins/EXP/exp_em/m

plugins/EXP/exp_em_multires/m

plugins/EXP/exp_ias/m

plugins/EXP/exp_ias_multires/m

plugins/FindSyntheticGravityData/m

plugins/FindSyntheticSource/m

plugins/FindSyntheticSourceLegacy

plugins/GMMClustering

plugins/GMMClustering/v2/m

plugins/GithubPusher/m

plugins/HBSampler/m

plugins/IASInversion/m

plugins/IASROIInversion/m

plugins/Kalman/m

plugins/LFBankTool/m

plugins/LFBankTool/m/lead_field_normalization_functions

plugins/LeadFieldProcessingTool

plugins/LeadFieldProcessingTool/m

plugins/MNETool/m

plugins/MUSIC

plugins/PlotMeshesProto

plugins/RAMUSInversion/m

plugins/RAMUSSampler/m

plugins/RAP-MUSIC

plugins/ReconstructionTool

plugins/ReconstructionTool/m

plugins/ReconstructionTool/m/apply_functions

plugins/SESAME/m

plugins/WireframeTool/m

plugins/ZeffiroESWorkbench/m

plugins/ZeffiroFilterTool/m

plugins/ZeffiroFilterTool/m/filter_bank

plugins/ZeffiroTopography/m

plugins/dataBank

plugins/dataBank/m

plugins/preconditioned_relaxation_tool/m

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.