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Zeffiro Forward and Inverse Interface for Brain Imaging

version 2.2.9 (86.9 MB) by Sampsa Pursiainen
Simple tool for finite element based forward and inverse simulations in electromagnetic brain imaging applications.

11 Downloads

Updated 07 May 2019

GitHub view license on GitHub

Zeffiro Interface (ZI), Sampsa Pursiainen © 2018, is an open source code
package constituting an accessible tool for finite element (FE) based
forward and inverse simulations in EEG/MEG and can be used also in other
bioelectromagnetical imaging applications targeting the brain. 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). 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 FE 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:

https://github.com/sampsapursiainen/zeffiro_interface/wiki

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 is 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.

Cite As

Sampsa Pursiainen (2019). Zeffiro Forward and Inverse Interface for Brain Imaging (https://www.github.com/sampsapursiainen/zeffiro_interface), GitHub. Retrieved .

Comments and Ratings (1)

More inverse tools.

Updates

2.2.9

Butterfly plot.

2.2.8

Corrections.

2.2.7

Corrections and a template for a 1 mm project added.

2.2.6

Minor fix of the startup script.

2.2.5

Segmentation import example for ASC (FreeSurfer) and DAT files added, import utility corrected.

2.2.4

Description.

2.2.3

Description.

2.2.2

Folder import utility for ASCII segmentation (DAT and ASC).

2.2.1

Description.

2.2.0

More compartments, Time series generator for connectivity analysis

2.1.1

Parcellation tool.

2.1.0

18-compartments, options to merge and invert meshes, when importing.

2.0.6

Missing plugin file added.

2.0.5

Flash-free time-lapses for r2018b and above.

2.0.4

Plugin utility added.

2.0.3

Bugs fixed.

2.0.2

Window configuration

2.0.1

Bugs fixed

2.0

New main window configuration.

1.0.12

New menus

1.0.11

Description and 3D plots.

1.0.10

Bugs corrected.

1.0.9

Corrected plot mesh routine.

1.0.8

Description

1.0.7

EIT and multiresolution solvers

1.0.6

Description

1.0.5

Gradiometer solver for MEG + EIT solver

1.0.4

Complete Electrode Model

1.0.3

More inverse tools.

1.0.2

Inverse tools update.

1.0.1

New inverse tools added.

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

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