|
Size: 4398
Comment:
|
Size: 16902
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Realistic head model: FEM with Duneuro = ''Authors: Takfarinas MEDANI,'' |
= Realistic head model: FEM with DUNEuro = '''[TUTORIAL UNDER REVISION]''' |
| Line 4: | Line 4: |
| 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'''). | ''Authors: [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], Juan Garcia-Prieto, Francois Tadel, Sophie Schrader, Anand Joshi, Christian Engwer, Carsten Wolters, John Mosher and Richard Leahy '' |
| Line 6: | Line 6: |
| refe to these point : http://duneuro.org/ | {{attachment:logo_duneuro.png||align="right",height="82",width="187"}} |
| Line 8: | Line 8: |
| and to the documentation from here : | This tutorial explains how to use [[http://duneuro.org/|DUNEuro]] to compute the forward model using the '''finite element method''' ('''FEM'''). The FEM methods use a realistic volume mesh of the head generated from the segmentation of the MRI. The FEM models provide more accurate results than the spherical forward models and more realistic geometry and tissue properties than the [[Tutorials/TutBem|BEM]] methods. |
| Line 10: | Line 10: |
| https://gitlab.dune-project.org/duneuro/duneuro/wikis/home | The scope of this page is limited to a '''basic example''' (head model with 3 layers). More advanced options for mesh generation and forward model computation are discussed in other tutorials: [[Tutorials/FemMesh|FEM mesh generation]], [[Tutorials/FemTensors|FEM tensors estimation]], [[Tutorials/FemMedianNerve|FEM median nerve example]]. We assume that you have already followed the [[Tutorials|introduction tutorials]], we will not discuss the general principles of forward modeling here. |
| Line 12: | Line 12: |
| Here we will describe the FEM and run some examples | <<TableOfContents(2,2)>> |
| Line 14: | Line 14: |
| == 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. |
== DUNEuro == '''[[http://duneuro.org/|DUNEuro]] '''is an open-source C++ software library for solving partial differential equations (PDE) in neurosciences using mesh-based methods. It is based on the''' [[https://www.dune-project.org/|DUNE library]] '''and its main features include solving the EEG and MEG forward problem and providing simulations for brain stimulation. |
| Line 17: | Line 17: |
| http://duneuro.org/ | As distributed on the [[http://gitlab.dune-project.org/duneuro/duneuro|DUNEuro GitLab]], the source code works only on Linux operating systems. Interfaces to Matlab and Python are possible, but you need to install and compile DUNEuro by yourself. For Brainstorm, we adapted this code and were able to generate '''binaries''' for the main operating systems''' '''(Windows, '''Linux '''and MacOS), which are '''downloaded automatically''' when needed as a [[Tutorials/Plugins|Brainstorm plugin]]. This project is available on our [[https://github.com/brainstorm-tools/bst-duneuro|GitHub repository bst-duneuro]]. We would like to thank the''' DUNEuro team '''for their help with this integration work: Carsten Wolters, Christian Engwer, Sophie Schrader, Andreas Nuessing, Tim Erdbruegger, Marios Antonakakis, Johannes Vorwerk & Maria Carla Piastra. ''' {{attachment:duneuroFromDune.JPG||width="546",height="187"}} ''' Please '''cite the following papers''' if you use this software in your work: * Medani T, Garcia-Prieto J, Tadel F, Schrader S, Antonakakis M, Joshi A, Engwer C, Wolters CH, Mosher JC, Leahy RM, [[https://doi.org/10.1117/12.2580935|Realistic head modeling of electromagnetic brain activity: an integrated Brainstorm-DUNEuro pipeline from MRI data to the FEM solutions]] ([[http://www.sci.utah.edu/~wolters/PaperWolters/2021/MedaniEtAl_SPIE_2021.pdf|preprint]]), SPIE Medical Imaging (2021) Publications that make use of, or extend the DUNEuro library (listed on the [[http://duneuro.org/|duneuro website]]): * Piastra MC, Nüßing A, Vorwerk J, Bornfleth H, Oostenveld R, Engwer C, Wolters CH, [[https://www.frontiersin.org/articles/10.3389/fnins.2018.00030/full|The Discontinuous Galerkin Finite Element Method for Solving the MEG and the combined MEG/EEG Forward Problem]], Frontiers in Neuroscience (2018) * Engwer C, Vorwerk J, Ludewig J, Wolters CH, [[https://epubs.siam.org/doi/abs/10.1137/15M1048392|A discontinuous Galerkin method to solve the EEG forward problem using the subtraction approach]], SIAM Journal on Scientific Computing (2017) * Nüßing A, Wolters CH, Brinck H, Engwer C, [[https://ieeexplore.ieee.org/document/7511781|The unfitted discontinuous Galerkin method for solving the EEG forward problem]], IEEE Transactions on Biomedical Engineering (2016)''' ''' |
| Line 20: | Line 34: |
| 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. | In order to reproduce the computation present below on your computer, you need to fulfill all the conditions listed below. Alternatively, you can read this page as a reference documentation about DUNEuro and not try to reproduce the results. |
| Line 22: | Line 36: |
| However if you want to use the source code of Duneuro you can visite: http://duneuro.org/ | * You have a working copy of Brainstorm installed on your computer. * You have already followed the [[https://neuroimage.usc.edu/brainstorm/Introduction|introduction tutorials]], at least until #23. * You have followed the tutorial [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy|EEG and Epilepsy]], as it is used for illustrating the computation. * '''DUNEuro''': Software installed automatically as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]]. * '''Iso2mesh''': Software installed automatically as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]]. |
| Line 24: | Line 42: |
| For the advanced user users, he main steps you need in order to compile for windows are listed here : | == FEM mesh == In order to use the FEM computations of the electromagnetic field (EEG/MEG), the volume mesh of the head is required. Brainstorm integrates most of the modern open-source tools to generate realistic head mesh, either from nested surface mesh or from individual MR images (T1 or T1 and T2). This tutorial describes only a simple approach based on three nested surfaces meshed in 3D with Iso2mesh. For the full list of available methods and description of options, please refer to the tutorial [[https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh|FEM mesh generation]].''' ''' |
| Line 26: | Line 45: |
| https://github.com/svdecomposer/brainstorm-duneuro | * Select the protocol TutorialEpilepsy, created while following the tutorial [[http://Tutorials/Epilepsy|EEG and epilepsy]]. * Go to the anatomy view. * Select the three [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem#BEM_surfaces|BEM surfaces]]: scalp, outer skull, inner skull. * Right-click > '''Generate FEM mesh''' > Iso2mesh-2021 > MergeMesh > Default options. <<BR>><<BR>> {{attachment:femMesh1.gif}} <<BR>> {{attachment:iso2mesh.gif}} ''' ''' * The FEM mesh appears in the database explorer after a short while. The first number indicates the number of vertices (i.e. nodes) of the tetrahedral mesh. To get the number of 3D elements (i.e. tetrahedrons) in this geometric model of the head: right-click on the file > File > View file contents. The structure of the file is describe in the tutorial [[https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh#On_the_hard_drive|FEM mesh generation]].<<BR>><<BR>> {{attachment:femMesh2.gif}} * Double-click on the FEM file to display it. From the Surface tab, you can change the resection locations by moving the bottom sliders, and you can control the display of each of the three layers individually. Click on the layer button in the toolbar, then adjust the color and transparency of the corresponding mesh. The figure below represents the FEM mesh in the center and the initial BEM layers on the right. <<BR>><<BR>> {{attachment:femMesh3.gif}} |
| Line 28: | Line 52: |
| We distribute the binary files for Windows/Ubunto 64bit systems, you don't need to installan extra Microsoft software package to run '''Duneuro.''' | == FEM forward model == The '''forward model''' (or '''head model''' in the Brainstorm documentation and interface) describes how the electric activity in the '''source space''' (the cortex surface or a regular grid of volume points) influences the electric potential (EEG) or magnetic fields (MEG) at the level of the '''sensors'''. The FEM method uses the '''tetrahedral mesh''' computed above to establish this relationship. ''' ''' |
| Line 30: | Line 56: |
| However, to use this pipline from Brainstorm you need to download these files (link to the binary fles and may be data ... ) | * Go the Anatomy view. Select the default FEM mesh and cortex surface you'd like to use for the computation (in case there is more than one in each category). The selected elements appear in green, double-click or right-click > Set as default to change the selection. * Go to the Functional view. Right-click on the channel file > '''Compute head model'''. <<BR>><<BR>>{{attachment:femCompute1.gif}} * Select '''MRI volume''', EEG: '''DUNEuro FEM''', '''Regular grid''': brain 5mm. <<BR>><<BR>>{{attachment:femCompute2.gif}} {{attachment:femCompute3.gif}} * Start the computation. If you selected the correct files, it should only take a few minutes. You may be prompted to download or update the bst-duneuro plugin. {{attachment:femCompute4.gif}} == Basic DUNEuro options == ''' <<BR>>''' At this level, the basic options are the list head's tissues and their conductivities. Brainstorm reads these parameters from the selected head model. * '''FEM tissues or layers: '''Brainstorm detects automatically the number of layers on your model. Users can select the desired layers to include for the FEM computation. According to the modalities, the recommended selections are: * For EEG: select all the layers * For MEG: use only select the inner layers (here brain) * For SEEG: use only the inner layers * For ECOG: use only the inner layers * Any combinations that include MEG: use all the layers In this case, there is Scalp (=head), Skull (=outer skull), and Brain (=inner skull). * '''FEM conductivities:''' Brainstorm detects automatically the number of layers and assigns the default isotropic value for each layer. However, you have the possibility to change these values according to your model. For advanced users, check the advanced section and a more detailed example at this page [[https://neuroimage.usc.edu/brainstorm/FemTensors|FEM tensor]]''.'' |
| Line 34: | Line 80: |
| == 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 ....). |
Brainstorm will download the latest version of the bst-duneuro binaries for your operating system from the Github, and install it in Brainstorm user folder (~username/.brainstorm/bst-duneuro/). The calculation of the head model will start automatically. You may wait for a very long time, which depends on the mesh resolution, the number of sensors, and of course the capacity of your computer. |
| Line 38: | Line 82: |
| This process will | So, be patient, it's worth it...''' '''''(for this model it's quite fast ... less than 10 min)'' |
| Line 40: | Line 84: |
| - merge the surfaces, | When it's finished, you have now a new head model for this subject in your database and can be used for the next steps/[[https://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel|(back to tutorial 20 : Head modeling)]] {{attachment:duneuroNode.JPG||width="400",height="150"}} |
| Line 42: | Line 86: |
| - check the self intersecting | === Anisotropy tensor from the DUNEuro options === In the case where the conductivity tensor are computed, Brainstorm detects and uses them for the FEM forward computation. |
| Line 44: | Line 89: |
| - fixe the size of the mesh | {{attachment:duneuroBasicOptionsTensor.JPG||width="300",height="300"}} |
| Line 46: | Line 91: |
| - generate the volum mesh | In this case, users can not change the conductivities values, since they are already computed as explained in this [[https://neuroimage.usc.edu/brainstorm/FemTensors|FEM tensor]]. |
| Line 48: | Line 93: |
| - visual checking ... | If at some points, for any reason, where users want to remove these FEM tensors, this can be done from the Brainstorm anatomy panel, select the FEM head model, right-click on the subject, and then "clear FEM tensor". |
| Line 50: | Line 95: |
| - TODO : may be we can add some mesh auqlity measures ?? | {{attachment:clearFemTensors.JPG||width="220",height="300"}} |
| Line 52: | Line 97: |
| '''<<TAG(Advanced)>>''' | == Advanced models and options == === DUNEuro advanced options panel [to be completed] === From the previous panel, for advanced duneuro panel, click on the button "Show details", the following panel is displayed. |
| Line 54: | Line 101: |
| === 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. |
{{attachment:duneuroAdvancedOptions.JPG||width="700",height="550"}} |
| Line 57: | Line 103: |
| ==> this depends lagely on the quality of the T1/T2 MRI image. | A set of advanced options are made available and can be easily changed. Here a short explanation is given for each option. |
| Line 59: | Line 105: |
| This step is based on the "roast" toolbox (link to roast : https://github.com/andypotatohy/roast | * '''FEM layers & conductivities''': same explanation as in the previous section. Moreover, in the case where the conductivity tensor are previously computed, Brainstorm detects these tensors and load them. In this case, the users can't change the conductivities scalar values, since they are not used. The following is displayed panel is displayed. |
| Line 61: | Line 107: |
| ) 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 solver type''': * CG or Continuous Galerkin: This is the standard Lagrangian method. |
| Line 63: | Line 110: |
| * DC or the Discontinuous Galerkin: | |
| Line 64: | Line 112: |
| In this version, only the Fitted FEM approaches are integrated, that require the FEM mesh of the head model. Unfitted methods are also available within DUNEuro, and will be integrated soon in Brainstorm. | |
| Line 65: | Line 114: |
| === Head model based on the level set approach === TODO and Validate |
* FEM source model: The list of the available source are * Venant * Subtraction * Partial Integration |
| Line 68: | Line 119: |
| == Forward model == === Head model === Number of layers, conductivity value, isotropy/anisotropy/ mesh resolution/ |
For more information about these methods, users can check this thesis (Vorwek thesis). |
| Line 72: | Line 121: |
| === Electrode model === Check the position of the electrodes and align to the head model (projection if needed) |
* Source space * Shrink source space: the location of dipoles are moved inward by the specified value in this field(in mm). * Force source space: this is required in the case where the dipoles are not within the GM matter. * Outputs options * Save transfer matrix: |
| Line 75: | Line 127: |
| === 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. |
All these parameters are stored and passed to the DUNEuro as a text file. This file is the main interface that passes the parameters from Brainstorm to DUNEuro. More details about the integration can be found in these links: |
| Line 78: | Line 129: |
| However, for the FEM model, more paramters could be tuned for the source model. | * GitHub repository for the [[https://github.com/brainstorm-tools/bst-duneuro|Brainstorm-DUNEuro]] compilation and integration * GitHub repository for the [[https://github.com/tmedani/duneuro_interface|matlab-duneuro interface]] * Brainstorm-DUNEuro integration discussions: * [[https://github.com/brainstorm-tools/brainstorm3/issues/185|Brainstorm-simbio/DUNEuro implementation]]/head model generation * [[https://github.com/brainstorm-tools/brainstorm3/issues/242|Integrate the DUNEuro FEM computation]] * [[https://github.com/brainstorm-tools/brainstorm3/pull/282|Genration of the FEM tensor]] * [[https://github.com/brainstorm-tools/brainstorm3/issues/302|Generation of the FEM source space]] |
| Line 80: | Line 137: |
| Choice of the source model : PI, Venant, Subtraction, Whitney | === FEM head model generation from MRI data === One of the advantages of the FEM is its ability to use more complex head models with realistic geometry. In this tutorial, we have shown a basic example, as an introduction. |
| Line 82: | Line 140: |
| Panel of the options choice that the user can select. (other wise we will set to default ) | For the generation of a more realistic head model, users can follow this [[https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh|FEM mesh tutorial]] to learn how to generate advanced FEM head models form magnetic resonance data. |
| Line 84: | Line 142: |
| === FEM conductivity tensors generation from DWI data === Among the advantages of the FEM, the use of tissue anisotropy (conductivity). The estimation of the tissue anisotropy is performed with the Brainsuite diffusion pipeline ([[http://brainsuite.org/processing/diffusion/|BDP]]). The diffusion tensor images (DTI) are estimated with Brainsuite from the diffusion-weighted images (DWI) and then converted to conductivity tensor using the [[https://www.pnas.org/content/98/20/11697|effective medieum approach]]. In order to use this tool, you need to install [[http://forums.brainsuite.org/download/|Brainsuite]] software, the rest of the process is distributed within bst-duneuro. |
|
| Line 85: | Line 145: |
| For more information, users can follow this [[https://neuroimage.usc.edu/brainstorm/FemTensors|FEM tensor]] [[https://neuroimage.usc.edu/brainstorm/FemTensors|tutorial]]. | |
| Line 86: | Line 147: |
| '''<<TAG(Advanced)>>''' | == Troubleshooting == DUNEuro binaries may crash for various reasons: we tried to list the possible causes here. Many FEM forward modeling issues are related with memory overload or extremely long computation times. Reducing the size of the problem may help in many cases. If you cannot find a solution, please post the full error message on the Brainstorm user forum (you can copy-paste the error message from the Matlab command window after closing the error message box). |
| Line 88: | Line 150: |
| === Advanced paramaters === - Solver parameters |
=== Grid error messages === * Error message: Coordinate is outside of the grid, or grid is not convex * Explanation: Some dipoles are probably outside of the cortex, users need to correct the source space. * Solution: ? |
| Line 91: | Line 155: |
| - Electrodes projection | === Remove the neck === One way to reduce the size of the forward problem is to decrease the number of FEM elements in the head model. When the field of the MRI is large, you may have the mesh of the neck and even the shoulders. In most cases, it is safe to remove the lower part of the FEM mesh, below the nose and the brainstem. Right-click on the FEM mesh > '''Resect Neck'''. |
| Line 93: | Line 158: |
| - maybe explain here the relevant option of the mini file ?? | {{attachment:resectNeck.JPG||width="600",height="150"}} Once the process is finished, a new FEM mesh appears in the database, with a tag "resect". The following figure shows the model before (743828 vertices / 4079587 elements) and after resection (613955 vertices / 3400957 elements). It will reduce the size of the problem by 20%. {{attachment:FemMeshAllandResect.JPG||width="600",height="150"}} |
| Line 96: | Line 165: |
| refer to : | ==== Related tutorials ==== * [[Tutorials/FemMesh|FEM mesh generation]] * [[Tutorials/FemTensors|FEM tensors estimation]] * [[Tutorials/FemMedianNerve|FEM median nerve example]] |
| Line 98: | Line 170: |
| http://duneuro.org/ | ==== DUNEuro references ==== * DUNEuro wiki: https://gitlab.dune-project.org/duneuro/duneuro/wikis/home * DUNEuro website: http://duneuro.org/ * List of the parameters: https://docs.google.com/spreadsheets/d/1MqURQsszn8Qj3-XRX_Z8qFFnz6Yl2-uYALkV-8pJVaM/edit#gid=0 |
| Line 100: | Line 175: |
| https://www.dune-project.org/ == Reported Errors & alternative solution == '''<<TAG(Advanced)>>''' == The MEEG forward problem with the FEM == == License == == Reference == |
==== Brainstorm-DUNEuro integration ==== * 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 REVISION]
Authors: Takfarinas Medani, Juan Garcia-Prieto, Francois Tadel, Sophie Schrader, Anand Joshi, Christian Engwer, Carsten Wolters, John Mosher and Richard Leahy
This tutorial explains how to use DUNEuro to compute the forward model using the finite element method (FEM). The FEM methods use a realistic volume mesh of the head generated from the segmentation of the MRI. The FEM models provide more accurate results than the spherical forward models and more realistic geometry and tissue properties than the BEM methods.
The scope of this page is limited to a basic example (head model with 3 layers). More advanced options for mesh generation and forward model computation are discussed in other tutorials: FEM mesh generation, FEM tensors estimation, FEM median nerve example. We assume that you have already followed the introduction tutorials, we will not discuss the general principles of forward modeling here.
Contents
DUNEuro
DUNEuro is an open-source C++ software library for solving partial differential equations (PDE) in neurosciences using mesh-based methods. It is based on the DUNE library and its main features include solving the EEG and MEG forward problem and providing simulations for brain stimulation.
As distributed on the DUNEuro GitLab, the source code works only on Linux operating systems. Interfaces to Matlab and Python are possible, but you need to install and compile DUNEuro by yourself. For Brainstorm, we adapted this code and were able to generate binaries for the main operating systems (Windows, Linux and MacOS), which are downloaded automatically when needed as a Brainstorm plugin. This project is available on our GitHub repository bst-duneuro.
We would like to thank the DUNEuro team for their help with this integration work: Carsten Wolters, Christian Engwer, Sophie Schrader, Andreas Nuessing, Tim Erdbruegger, Marios Antonakakis, Johannes Vorwerk & Maria Carla Piastra.
Please cite the following papers if you use this software in your work:
Medani T, Garcia-Prieto J, Tadel F, Schrader S, Antonakakis M, Joshi A, Engwer C, Wolters CH, Mosher JC, Leahy RM, Realistic head modeling of electromagnetic brain activity: an integrated Brainstorm-DUNEuro pipeline from MRI data to the FEM solutions (preprint), SPIE Medical Imaging (2021)
Publications that make use of, or extend the DUNEuro library (listed on the duneuro website):
Piastra MC, Nüßing A, Vorwerk J, Bornfleth H, Oostenveld R, Engwer C, Wolters CH, The Discontinuous Galerkin Finite Element Method for Solving the MEG and the combined MEG/EEG Forward Problem, Frontiers in Neuroscience (2018)
Engwer C, Vorwerk J, Ludewig J, Wolters CH, A discontinuous Galerkin method to solve the EEG forward problem using the subtraction approach, SIAM Journal on Scientific Computing (2017)
Nüßing A, Wolters CH, Brinck H, Engwer C, The unfitted discontinuous Galerkin method for solving the EEG forward problem, IEEE Transactions on Biomedical Engineering (2016)
Requirements
In order to reproduce the computation present below on your computer, you need to fulfill all the conditions listed below. Alternatively, you can read this page as a reference documentation about DUNEuro and not try to reproduce the results.
- You have a working copy of Brainstorm installed on your computer.
You have already followed the introduction tutorials, at least until #23.
You have followed the tutorial EEG and Epilepsy, as it is used for illustrating the computation.
DUNEuro: Software installed automatically as a Brainstorm plugin.
Iso2mesh: Software installed automatically as a Brainstorm plugin.
FEM mesh
In order to use the FEM computations of the electromagnetic field (EEG/MEG), the volume mesh of the head is required. Brainstorm integrates most of the modern open-source tools to generate realistic head mesh, either from nested surface mesh or from individual MR images (T1 or T1 and T2). This tutorial describes only a simple approach based on three nested surfaces meshed in 3D with Iso2mesh. For the full list of available methods and description of options, please refer to the tutorial FEM mesh generation.
Select the protocol TutorialEpilepsy, created while following the tutorial EEG and epilepsy.
- Go to the anatomy view.
Select the three BEM surfaces: scalp, outer skull, inner skull.
Right-click > Generate FEM mesh > Iso2mesh-2021 > MergeMesh > Default options.
The FEM mesh appears in the database explorer after a short while. The first number indicates the number of vertices (i.e. nodes) of the tetrahedral mesh. To get the number of 3D elements (i.e. tetrahedrons) in this geometric model of the head: right-click on the file > File > View file contents. The structure of the file is describe in the tutorial FEM mesh generation.
Double-click on the FEM file to display it. From the Surface tab, you can change the resection locations by moving the bottom sliders, and you can control the display of each of the three layers individually. Click on the layer button in the toolbar, then adjust the color and transparency of the corresponding mesh. The figure below represents the FEM mesh in the center and the initial BEM layers on the right.
FEM forward model
The forward model (or head model in the Brainstorm documentation and interface) describes how the electric activity in the source space (the cortex surface or a regular grid of volume points) influences the electric potential (EEG) or magnetic fields (MEG) at the level of the sensors. The FEM method uses the tetrahedral mesh computed above to establish this relationship.
Go the Anatomy view. Select the default FEM mesh and cortex surface you'd like to use for the computation (in case there is more than one in each category). The selected elements appear in green, double-click or right-click > Set as default to change the selection.
Go to the Functional view. Right-click on the channel file > Compute head model.
Select MRI volume, EEG: DUNEuro FEM, Regular grid: brain 5mm.
Start the computation. If you selected the correct files, it should only take a few minutes. You may be prompted to download or update the bst-duneuro plugin.
Basic DUNEuro options
At this level, the basic options are the list head's tissues and their conductivities. Brainstorm reads these parameters from the selected head model.
FEM tissues or layers: Brainstorm detects automatically the number of layers on your model. Users can select the desired layers to include for the FEM computation. According to the modalities, the recommended selections are:
- For EEG: select all the layers
- For MEG: use only select the inner layers (here brain)
- For SEEG: use only the inner layers
- For ECOG: use only the inner layers
- Any combinations that include MEG: use all the layers
FEM conductivities: Brainstorm detects automatically the number of layers and assigns the default isotropic value for each layer. However, you have the possibility to change these values according to your model.
For advanced users, check the advanced section and a more detailed example at this page FEM tensor.
Brainstorm will download the latest version of the bst-duneuro binaries for your operating system from the Github, and install it in Brainstorm user folder (~username/.brainstorm/bst-duneuro/). The calculation of the head model will start automatically. You may wait for a very long time, which depends on the mesh resolution, the number of sensors, and of course the capacity of your computer.
So, be patient, it's worth it... (for this model it's quite fast ... less than 10 min)
When it's finished, you have now a new head model for this subject in your database and can be used for the next steps/(back to tutorial 20 : Head modeling) ![[ATTACH]](/brainstorm/Tutorials/Duneuro?action=AttachFile&do=upload_form&ticket=0067839d9b.2d15d58958b74c93627241b3c373c46e8ffe5cfc&target=duneuroNode.JPG "[ATTACH]"){kind=small}
Anisotropy tensor from the DUNEuro options
In the case where the conductivity tensor are computed, Brainstorm detects and uses them for the FEM forward computation.
![[ATTACH]](/brainstorm/Tutorials/Duneuro?action=AttachFile&do=upload_form&ticket=0067839d9b.2d15d58958b74c93627241b3c373c46e8ffe5cfc&target=duneuroBasicOptionsTensor.JPG "[ATTACH]"){kind=small}
In this case, users can not change the conductivities values, since they are already computed as explained in this FEM tensor.
If at some points, for any reason, where users want to remove these FEM tensors, this can be done from the Brainstorm anatomy panel, select the FEM head model, right-click on the subject, and then "clear FEM tensor".
Advanced models and options
DUNEuro advanced options panel [to be completed]
From the previous panel, for advanced duneuro panel, click on the button "Show details", the following panel is displayed.
![[ATTACH]](/brainstorm/Tutorials/Duneuro?action=AttachFile&do=upload_form&ticket=0067839d9b.2d15d58958b74c93627241b3c373c46e8ffe5cfc&target=duneuroAdvancedOptions.JPG "[ATTACH]"){kind=small}
A set of advanced options are made available and can be easily changed. Here a short explanation is given for each option.
FEM layers & conductivities: same explanation as in the previous section. Moreover, in the case where the conductivity tensor are previously computed, Brainstorm detects these tensors and load them. In this case, the users can't change the conductivities scalar values, since they are not used. The following is displayed panel is displayed.
FEM solver type:
- CG or Continuous Galerkin: This is the standard Lagrangian method.
- DC or the Discontinuous Galerkin:
In this version, only the Fitted FEM approaches are integrated, that require the FEM mesh of the head model. Unfitted methods are also available within DUNEuro, and will be integrated soon in Brainstorm.
- FEM source model: The list of the available source are
- Venant
- Subtraction
- Partial Integration
For more information about these methods, users can check this thesis (Vorwek thesis).
- Source space
- Shrink source space: the location of dipoles are moved inward by the specified value in this field(in mm).
- Force source space: this is required in the case where the dipoles are not within the GM matter.
- Outputs options
- Save transfer matrix:
All these parameters are stored and passed to the DUNEuro as a text file. This file is the main interface that passes the parameters from Brainstorm to DUNEuro. More details about the integration can be found in these links:
GitHub repository for the Brainstorm-DUNEuro compilation and integration
GitHub repository for the matlab-duneuro interface
- Brainstorm-DUNEuro integration discussions:
FEM head model generation from MRI data
One of the advantages of the FEM is its ability to use more complex head models with realistic geometry. In this tutorial, we have shown a basic example, as an introduction.
For the generation of a more realistic head model, users can follow this FEM mesh tutorial to learn how to generate advanced FEM head models form magnetic resonance data.
FEM conductivity tensors generation from DWI data
Among the advantages of the FEM, the use of tissue anisotropy (conductivity). The estimation of the tissue anisotropy is performed with the Brainsuite diffusion pipeline (BDP). The diffusion tensor images (DTI) are estimated with Brainsuite from the diffusion-weighted images (DWI) and then converted to conductivity tensor using the effective medieum approach. In order to use this tool, you need to install Brainsuite software, the rest of the process is distributed within bst-duneuro.
For more information, users can follow this FEM tensor tutorial.
Troubleshooting
DUNEuro binaries may crash for various reasons: we tried to list the possible causes here. Many FEM forward modeling issues are related with memory overload or extremely long computation times. Reducing the size of the problem may help in many cases. If you cannot find a solution, please post the full error message on the Brainstorm user forum (you can copy-paste the error message from the Matlab command window after closing the error message box).
Grid error messages
- Error message: Coordinate is outside of the grid, or grid is not convex
- Explanation: Some dipoles are probably outside of the cortex, users need to correct the source space.
- Solution: ?
Remove the neck
One way to reduce the size of the forward problem is to decrease the number of FEM elements in the head model. When the field of the MRI is large, you may have the mesh of the neck and even the shoulders. In most cases, it is safe to remove the lower part of the FEM mesh, below the nose and the brainstem. Right-click on the FEM mesh > Resect Neck.
Once the process is finished, a new FEM mesh appears in the database, with a tag "resect". The following figure shows the model before (743828 vertices / 4079587 elements) and after resection (613955 vertices / 3400957 elements). It will reduce the size of the problem by 20%.
Additional documentation
Related tutorials
DUNEuro references
DUNEuro wiki: https://gitlab.dune-project.org/duneuro/duneuro/wikis/home
DUNEuro website: http://duneuro.org/
List of the parameters: https://docs.google.com/spreadsheets/d/1MqURQsszn8Qj3-XRX_Z8qFFnz6Yl2-uYALkV-8pJVaM/edit#gid=0