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| = Realistic head model: FEM with Duneuro = ''Authors: Takfarinas MEDANI, Juan, Sophie, Christian, Carsten, John, Richard '' |
= Realistic head model: FEM with DUNEuro = '''[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE]''' |
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| This tutorial explains how to use brainstorm-dueneuro to compute the forward model. | ''Authors: Takfarinas, Juan, François ...Sophie, Johannes, Maria, Christian, Carsten, John, Richard ? '' |
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| This forward model uses a finite element element method (FEM) and was developed by the '''...(l''''''ink)'''. 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 [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG and epilepsy]] or similar data ('''todo'''). | This tutorial explains how to use brainstorm-dueneuro to compute the head model using the finite element method, implemented in the Duneuro software. |
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| refe to these point : http://duneuro.org/ | This forward model uses a finite element element method (FEM) implemented within the [[http://duneuro.org/|Duneuro]] software. More documentation could be found on this [[https://gitlab.dune-project.org/duneuro/duneuro/wikis/home|gitlab page]]. |
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| and to the documentation from here : | The FEM methods use the realistic volume mesh of the head model genertaed from the segmentation of the magnetic reasonance images (MRI). The goal of the forward solution is, mostly for '''EEG users (and for sEEG/ECOG)''', to provide more accurate results than the spherical models and more realistic geometry than the BEM. |
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| https://gitlab.dune-project.org/duneuro/duneuro/wikis/home | In this tutorial we will describe the software requirement to use the DUNEuro computation from brainstrom and examples on the FEM computation through the graphical interface. |
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| Here we will describe the FEM and run some examples | == DUNEuro == [[http://duneuro.org/|DUNEuro]] is an open-source C++ software library for solving partial differential equations (PDE) in neurosciences using mesh bases methods. It is based on the [[https://www.dune-project.org/|DUNE library]] and its main features that include solving the electroencephalography (EEG) and magnetoencephalography (MEG) forward problem and providing simulations for brain stimulation. {{attachment:duneuroFromDune2.png|height="50",width="120"}} |
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| == 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. |
== Citing DUNEuro == If you use '''DUNEuro-'''Brainstorm, please cite the following articles in your publications: |
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| http://duneuro.org/ | Andreas Nüßing, Maria Carla Piastra, Sophie Schrader, Tuuli Miinalainen, Sampsa Pursiainen, Heinrich Brinck, Carsten H. Wolters, Christian Engwer ''"duneuro - A software toolbox for forward modeling in neuroscience"'' under review ''"The Brainstrom-Duneuro : friendely interface for the EEG/MEG with the Finite Elelemt Method"'' under writing <<BR>><<BR>> |
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| 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. | === DUNEuro for the FEM computation === Th DUNEuro binaries are distributed within the [[https://github.com/brainstorm-tools/bst-duneuro|bst-duneuro toolbox]]. These binaries are adapted and tested for Windows, MAC and Ubunto 64bit systems. Therefore you don't need to install any extra software package to run the FEM computation'''.''' |
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| However if you want to use the source code of Duneuro you can visite: http://duneuro.org/ | Brainstromwill download and istall the [[https://github.com/brainstorm-tools/bst-duneuro|bst-duneuro toolbox]] when it'is needed. |
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| For the advanced user users, he main steps you need in order to compile for windows are listed here : | <<BR>>'''<<TAG(Advanced)>>''' <<BR>> |
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| https://github.com/svdecomposer/brainstorm-duneuro | DUNEuro software is build on top of the DUNE Library, 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), therfore it can be easily used from Matlab without the need to install and compile the tediuos Dune and Duneuro libraries on your computer. |
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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.''' | If you do so, we have develloped an alternative way to install and generate the binaries for the main platforms, the main steps you need are explained [[https://github.com/brainstorm-tools/bst-duneuro|here]]. |
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| However, to use this pipline from Brainstorm you need to download these files (link to the binary fles and may be data ... ) | === FEM Mesh generation & processing === In order to used the FEM computation of the electromagnetic field, the volume mesh of the head is required. Brainstorm can generates realistric head mesh model from MRI data, in order to do the the SimNibs software shoud be installed in your computer. |
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| The FEM mesh visualisation and some of the mesh processing integrated with brainstorm requires the installation of the [[http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Download|iso2mesh]] toolbox. ==== SimNIBS Installation ==== Please follow the instructions on this [[https://simnibs.github.io/simnibs/build/html/installation/simnibs_installer.html|webapge]]''__ (new brainstom page that explain how to generate the head model is under development)__'' ==== Iso2Mesh Installation ==== If iso2mesh is not installed in your computer, Brainstrom will download the last release from this [[https://neuroimage.usc.edu/brainstorm/http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Download|webpage]] and install it when it'is needed. However, you can also download the iso2mesh from the [[https://github.com/fangq/iso2mesh|github]] and add it to your matlab path. ==== Brainsuite Installation [TODO] ==== |
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| === Volume mesh generation from Brainstorm === The most modern software that are used to generate the volume mesh head model are integrated within brainstorm with an easy graphical interface to use call these tools. Right click on the subject and then "Generate FEM Mesh" {{attachment:menuGenerateFemMesh.PNG|height="40",width="150"}} The available options are : . {{attachment:FemMeshMethods.PNG|height="50",width="100"}} "Iso2mesh" : This option merges the brainstorm surfaces available on the subject and then generarte the tetrahedral mesh. "Brain2Mesh" : This options uses the MRIs available on the subjects, then it calls the SPM segmentation of the volume into 5 tissus (white, gray, scf, skull and skin). After that it converts into a tetrahedral mesh. "SimNibs" : The recommended option, it calls the headreco {ref} and generate a FEM head model "FieldTrip" : (in progress) "Roast" : (in progress) "headreco" : https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html This function is part of the SimNibs software: https://simnibs.github.io/simnibs/build/html/index.html === headreco === The headreco function is fully integrated to brainstorm. With this option, brainstorm can reconstructs a tetrahedral head mesh from T1- and T2-weighted structural MR images. It runs also with only a T1w image, but it will achieve more reliable skull segmentations when a T2w image is supplied. === Surface mesh generation from volume mesh === |
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| === 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. |
=== 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. |
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| ==> this depends lagely on the quality of the T1/T2 MRI image. | ==> this depends lagely on the quality of the T1/T2 MRI image(https://simnibs.github.io/simnibs/build/html/tutorial/head_meshing.html). |
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| * f there is a MRI file with the string "T2" in the subject anatomy folder, it will use it * Otherwise, if you select explicitly two MRI files with CTRL+Click, it will use the first one as the T1 and the second one as the T2 (this needs to be documented in the tutorial) === 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 ... ) https://github.com/brainstorm-tools/brainstorm3/issues/185#issuecomment-576749612 |
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| == Forward model == | if users want to use freesurfer and simnibs, the priority is given to freesurfer, then load the fs files, then call simnibs headmodel generation from t1/t2. == FEM computation and interface to DUNEuro == |
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| https://simnibs.github.io/simnibs/build/html/index.html |
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simnibs pblm : https://simnibs.github.io/simnibs/build/html/installation/throubleshooting.html |
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| == Additional documentation == https://github.com/brainstorm-tools/bst-duneuro/issues/1 https://github.com/brainstorm-tools/brainstorm3/issues/242 https://github.com/brainstorm-tools/brainstorm3/issues/185 |
Realistic head model: FEM with DUNEuro
[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE]
Authors: Takfarinas, Juan, François ...Sophie, Johannes, Maria, 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) implemented within the Duneuro software. More documentation could be found on this gitlab page.
The FEM methods use the realistic volume mesh of the head model genertaed from the segmentation of the magnetic reasonance images (MRI). The goal of the forward solution is, mostly for EEG users (and for sEEG/ECOG), to provide more accurate results than the spherical models and more realistic geometry than the BEM.
In this tutorial we will describe the software requirement to use the DUNEuro computation from brainstrom and examples on the FEM computation through the graphical interface.
DUNEuro
DUNEuro is an open-source C++ software library for solving partial differential equations (PDE) in neurosciences using mesh bases methods. It is based on the DUNE library and its main features that include solving the electroencephalography (EEG) and magnetoencephalography (MEG) forward problem and providing simulations for brain stimulation. ![[ATTACH]](/brainstorm/Tutorials/Duneuro?action=AttachFile&do=upload_form&ticket=0067716136.fd0394389744385517ee81dc14bc12b1107ea507&target=duneuroFromDune2.png "[ATTACH]"){kind=small}
Citing DUNEuro
If you use DUNEuro-Brainstorm, please cite the following articles in your publications:
Andreas Nüßing, Maria Carla Piastra, Sophie Schrader, Tuuli Miinalainen, Sampsa Pursiainen, Heinrich Brinck, Carsten H. Wolters, Christian Engwer
"duneuro - A software toolbox for forward modeling in neuroscience" under review
"The Brainstrom-Duneuro : friendely interface for the EEG/MEG with the Finite Elelemt Method"
under writing
Requirements
DUNEuro for the FEM computation
Th DUNEuro binaries are distributed within the bst-duneuro toolbox. These binaries are adapted and tested for Windows, MAC and Ubunto 64bit systems. Therefore you don't need to install any extra software package to run the FEM computation.
Brainstromwill download and istall the bst-duneuro toolbox when it'is needed.
DUNEuro software is build on top of the DUNE Library, 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), therfore it can be easily used from Matlab without the need to install and compile the tediuos Dune and Duneuro libraries on your computer.
If you do so, we have develloped an alternative way to install and generate the binaries for the main platforms, the main steps you need are explained here.
FEM Mesh generation & processing
In order to used the FEM computation of the electromagnetic field, the volume mesh of the head is required. Brainstorm can generates realistric head mesh model from MRI data, in order to do the the SimNibs software shoud be installed in your computer.
The FEM mesh visualisation and some of the mesh processing integrated with brainstorm requires the installation of the iso2mesh toolbox.
SimNIBS Installation
Please follow the instructions on this webapge (new brainstom page that explain how to generate the head model is under development)
Iso2Mesh Installation
If iso2mesh is not installed in your computer, Brainstrom will download the last release from this webpage and install it when it'is needed. However, you can also download the iso2mesh from the github and add it to your matlab path.
Brainsuite Installation [TODO]
FEM surfaces / Volume generation
Volume mesh generation from Brainstorm
The most modern software that are used to generate the volume mesh head model are integrated within brainstorm with an easy graphical interface to use call these tools.
Right click on the subject and then "Generate FEM Mesh"
![[ATTACH]](/brainstorm/Tutorials/Duneuro?action=AttachFile&do=upload_form&ticket=0067716136.fd0394389744385517ee81dc14bc12b1107ea507&target=menuGenerateFemMesh.PNG "[ATTACH]"){kind=small}
The available options are :
![[ATTACH]](/brainstorm/Tutorials/Duneuro?action=AttachFile&do=upload_form&ticket=0067716136.fd0394389744385517ee81dc14bc12b1107ea507&target=FemMeshMethods.PNG "[ATTACH]"){kind=small}
"Iso2mesh" : This option merges the brainstorm surfaces available on the subject and then generarte the tetrahedral mesh.
"Brain2Mesh" : This options uses the MRIs available on the subjects, then it calls the SPM segmentation of the volume into 5 tissus (white, gray, scf, skull and skin). After that it converts into a tetrahedral mesh.
"SimNibs" : The recommended option, it calls the headreco {ref} and generate a FEM head model
"FieldTrip" : (in progress) "Roast" : (in progress)
"headreco" :
https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html
This function is part of the SimNibs software:
https://simnibs.github.io/simnibs/build/html/index.html
headreco
The headreco function is fully integrated to brainstorm. With this option, brainstorm can reconstructs a tetrahedral head mesh from T1- and T2-weighted structural MR images. It runs also with only a T1w image, but it will achieve more reliable skull segmentations when a T2w image is supplied.
Surface mesh generation from volume mesh
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(https://simnibs.github.io/simnibs/build/html/tutorial/head_meshing.html).
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.
- f there is a MRI file with the string "T2" in the subject anatomy folder, it will use it
- Otherwise, if you select explicitly two MRI files with CTRL+Click, it will use the first one as the T1 and the second one as the T2 (this needs to be documented in the tutorial)
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 ... )
https://github.com/brainstorm-tools/brainstorm3/issues/185#issuecomment-576749612
Head model based on the level set approach
TODO and Validate
if users want to use freesurfer and simnibs, the priority is given to freesurfer, then load the fs files, then call simnibs headmodel generation from t1/t2.
FEM computation and interface 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 :
https://simnibs.github.io/simnibs/build/html/index.html
Reported Errors & alternative solution
simnibs pblm :
https://simnibs.github.io/simnibs/build/html/installation/throubleshooting.html
The MEEG forward problem with the FEM
License
Reference
Additional documentation
https://github.com/brainstorm-tools/bst-duneuro/issues/1