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| ''Authors: Takfarinas MEDANI,'' | '''[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE]''' ''Authors: Takfarinas,... Juan, Sophie, Christian, Carsten, John, Richard ? '' This tutorial explains how to use brainstorm-dueneuro to compute the forward model. |
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| Duneuro is build on top of DUNE Library, at this time (sept 2019) these libraries work only on Linux systems. However we are able to run generate binaries for windows and can be easily used from Matlab for all platforms. | Duneuro is build on top of DUNE Library, at this time (sept 2019) the code source works only on Linux systems. However we are able to generate the binaries for windows, therefor it can be easily used from Matlab for all platforms. |
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| We also put here : The main steps you need in order to compile for windows are listed here : |
For the advanced user users, he main steps you need in order to compile for windows are listed here : |
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| We distribute the binary files for Windows/Ubunto 64bit systems, you don't need to installan extra Microsoft software package to run '''Duneuro''' | We distribute the binary files for Windows/Ubunto 64bit systems, you don't need to installan extra Microsoft software package to run '''Duneuro.''' |
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| . Microsoft Visual C++ 2010 Redistributable Package (x64). | However, to use this pipline from Brainstorm you need to download these files (link to the binary fles and may be data ... ) |
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| '''<<TAG(Advanced)>>''' | |
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| You can also generate your own FEM head model and use it from brainstorm to ciompute the forward problem. However the automatic head model generation from from imaging techniques are not accurate and most of the time visual checking are needed and manual correction are required. ==> this depends lagely on the quality of the T1/T2 MRI image. This step is based on the "roast" toolbox (link to roast : https://github.com/andypotatohy/roast ) that we adapted for the MEEG forward computation. If you want to generate your own FEM head model from an MRI, you will need to download these file (link), then run the bst process as explained here. |
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| TODO and Validate | |
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| Number of layers, conductivity value, | Number of layers, conductivity value, isotropy/anisotropy/ mesh resolution/ |
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| Similarly to the spherical nad BEM head model, the source position are defined on the cortex surface vertices. We can either define a contraned or not constrained orientation. However, for the FEM model, more paramters could be tuned for the source model. Choice of the source model : PI, Venant, Subtraction, Whitney Panel of the options choice that the user can select. (other wise we will set to default ) '''<<TAG(Advanced)>>''' |
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| - Solver parameters - Electrodes projection - maybe explain here the relevant option of the mini file ?? |
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| refer to : http://duneuro.org/ https://www.dune-project.org/ |
Realistic head model: FEM with Duneuro
[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE]
Authors: Takfarinas,... Juan, Sophie, Christian, Carsten, John, Richard ?
This tutorial explains how to use brainstorm-dueneuro to compute the forward model.
This forward model uses a finite element element method (FEM) and was developed by the ...(link). It uses the volume mesh of the realistic head model. The goal of this forward solution is mostly for EEG users, to provide more accurate results than the spherical models and more complex geometry than the BEM. It is not necessary for MEG users, as the "overlapping spheres" method gives similar results but much faster. This method is illustrated using the tutorial EEG and epilepsy or similar data (todo).
refe to these point : http://duneuro.org/
and to the documentation from here :
https://gitlab.dune-project.org/duneuro/duneuro/wikis/home
Here we will describe the FEM and run some examples
Duneuro
duneuro is an open-source C++ software library for solving partial differential equations in neurosciences using mesh bases methods. It is based on the DUNE library and its main features include solving the electroencephalography (EEG) and magnetoencephalography (MEG) forward problem and providing simulations for brain stimulation.
Requirements
Duneuro is build on top of DUNE Library, at this time (sept 2019) the code source works only on Linux systems. However we are able to generate the binaries for windows, therefor it can be easily used from Matlab for all platforms.
However if you want to use the source code of Duneuro you can visite: http://duneuro.org/
For the advanced user users, he main steps you need in order to compile for windows are listed here :
https://github.com/svdecomposer/brainstorm-duneuro
We distribute the binary files for Windows/Ubunto 64bit systems, you don't need to installan extra Microsoft software package to run Duneuro.
However, to use this pipline from Brainstorm you need to download these files (link to the binary fles and may be data ... )
FEM surfaces / Volume generation
Volume generation from surface files
In this part you can generate your FEM mesh from surfaces that you can get fron the segmentation software (brainSuite, FreeSurfer ....).
This process will
- merge the surfaces,
- check the self intersecting
- fixe the size of the mesh
- generate the volum mesh
- visual checking ...
- TODO : may be we can add some mesh auqlity measures ??
Volume generation from T1 MRI data
You can also generate your own FEM head model and use it from brainstorm to ciompute the forward problem. However the automatic head model generation from from imaging techniques are not accurate and most of the time visual checking are needed and manual correction are required.
==> this depends lagely on the quality of the T1/T2 MRI image.
This step is based on the "roast" toolbox (link to roast : https://github.com/andypotatohy/roast
) that we adapted for the MEEG forward computation. If you want to generate your own FEM head model from an MRI, you will need to download these file (link), then run the bst process as explained here.
Head model based on the level set approach
TODO and Validate
Forward model
Head model
Number of layers, conductivity value, isotropy/anisotropy/ mesh resolution/
Electrode model
Check the position of the electrodes and align to the head model (projection if needed)
Source model
Similarly to the spherical nad BEM head model, the source position are defined on the cortex surface vertices. We can either define a contraned or not constrained orientation.
However, for the FEM model, more paramters could be tuned for the source model.
Choice of the source model : PI, Venant, Subtraction, Whitney
Panel of the options choice that the user can select. (other wise we will set to default )
Advanced paramaters
- Solver parameters
- Electrodes projection
- maybe explain here the relevant option of the mini file ??
Additional documentation
refer to :
Reported Errors & alternative solution
The MEEG forward problem with the FEM
License