Realistic head model: FEM with Duneuro
[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE]
Authors: Takfarinas, Juan, Francois, Sophie, Maria, Johannes, Christian, Carsten, John, Richard ?
This tutorial explains how to use brainstorm-dueneuro to compute the head model using the finite element method, implemented in the Duneuro software.
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 (September 2019) the source code works only on Linux operating systems. However we are able to generate the binaries for the main platforms (windows 64, Linux and Mac), therefor it can be easily used from Matlab for all platforms without the need to install and compile the tidiuos CPP library of DUNE and DUNEURO.
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 the bst-duneuro toolbox (ref) that interface brainstorm to duneuro.
The FEM mesh visualisation and some mesh processing requires the installation of the iso2mesh toolbox (link). If you want to work on offline, you can download it and add it to your matlab path. If it's not installed, Brainstrom will download and istall this toolbox when it needed.
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/T2 MRI data
You can also generate your own FEM head model and then load it to brainstorm. 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.
FEM Head model generation with SimNibs
This method used the SimNibs software. So to call this process, you need to download and install the SimNibs software, the process of the installation is explained in the SimNibs webpage : https://simnibs.github.io/simnibs/build/html/installation/simnibs_installer.html.
When you have installed SimNibs, Brainstorm can call the main function used for the mesh generation frm the main graphical interface. Depemding on your computer performances, this process will take between 2 to 5 hours. We highly recommend to close all other running process and application on our computer in order to speed this process.
- Explain here the main steps with screenshots :
1- Create new subject within the current protocole
2- Load the T1 of the subject to the brainstorm database.
3- Associate a T2 mri to the subject if it's available (this is better for csf/skull/scalp segmentation)
4- Right click on the subject, select the "Generate FEM mesh"
- Select "SIMNIBS", and choose "Tetrahedral element" and keep the other options to the default value.
5- When this process is finished, a new node will appear in the data base, which hase he name "FEM xxxV, (simNibs, yLayers)". This is the FEM mesh model generated from the T1.
FEM Head model template
- Load the FEM volumic mesh (template created from ICBM T1 MRI using SimNibs)
- Load the surface mesh (template created also from ICBM using ICBM ) and then generates the volume mesh (either tetra or hexa) by calling the tetgen process cia iso2mesh toolbox (if hexa are desired, the tetra mesh will be converted to hexa ... )
Head model based on the level set approach
TODO and Validate
FEM computation and unterface to DUNEuro
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