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| This forward model uses a symmetric boundary element method (symmetric BEM) and was developed by the French public research institute INRIA ([[http://www-sop.inria.fr/athena/software/OpenMEEG/|website]]). It uses three realistic layers (scalp, inner skull, outer skull). The goal of this forward solution is mostly for EEG users, to provide a better model than the existing "3-shell sphere". It is not necessary for MEG users, as the "overlapping spheres" method gives very similar results but much faster. Nevertheless, for demonstration purpose, we are going to compute this solution on MEG recordings. | ''Authors: Francois Tadel, Alexandre Gramfort'' This forward model uses a symmetric boundary element method (symmetric BEM) and was developed by the French public research institute INRIA ([[http://openmeeg.github.io|website]]). It uses three realistic layers (scalp, inner skull, outer skull). The goal of this forward solution is mostly for '''EEG users''', to provide a better model than the existing "3-shell sphere". It is not necessary for MEG users, as the "overlapping spheres" method gives relatively similar results but faster. Nevertheless, for demonstration purpose or in case you want to use the same head model for both EEG and MEG data, we are going to compute this solution on MEG recordings, using the existing TutorialCTF protocol. {{attachment:openmeeg.gif||height="75px",width="274px"}} <<TableOfContents(2,2)>> == Requirements == On Windows 64bit systems, you need to install an extra Microsoft software package to run OpenMEEG: Microsoft Visual C++ 2010 Redistributable Package (x64).<<BR>>http://www.microsoft.com/en-us/download/details.aspx?id=14632 |
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| We need three realistic layers extracted from the subject's MRI (scalp, inner skull, outer skull), plus the source space (cortical surface). Those layers are sometimes complicated to generate. In the case you do not have any way to calculate the inner skull and outer skull surfaces, Brainstorm can generate rough approximations based on the subject's cortex and head surfaces and Colin27's inner and outer skull surfaces. | We need three realistic layers extracted from the subject's MRI (scalp, inner skull, outer skull), plus the source space (cortical surface). Those layers are sometimes complicated to generate. In the case you do not have any way to calculate the inner skull and outer skull surfaces, Brainstorm can generate rough approximations based on the subject's cortex and head surfaces and Colin27's inner and outer skull surfaces.The surfaces created with Brainstorm are by construction non-intersecting. |
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| 1. Select the TutorialCTF protocol 1. Go to the anatomy view (first button on top of the database explorer) 1. Right-click on Subject01 > Generate BEM surfaces...You can set the approximate number of vertices you want for each layer. For the example, leave the default parameters and click on Ok. 1. Note that those values are very low and could lead to incoherent results. However, using more vertices on each layer can increase a lot the amount of memory necessary and the computation time. If you can afford it computationally, you should use a minimum of '''2000 vertices''' per layer. Note that you may not get the number of vertices you are asking for, the algorithm generating those surfaces uses a fixed set of apolar spheres with the following number of vertices: 273, 362, 482, 642, 812, 1082, 1442, 1922, 2432, 2562, 3242, 4322...<<BR>><<BR>> {{attachment:bemPopup.gif}} {{attachment:bemOptions.gif}} 1. At the end of the process, three new surfaces are added to the database:<<BR>><<BR>> {{attachment:bemFiles.gif}} {{attachment:bem3d.gif}} |
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| == Forward model == 1. Switch to the view "Functional data (sorted by subjects)" 1. Right-click on Subject01 / Right > Compute head model. Select OpenMEEG BEM in the list. Click on Run.<<BR>><<BR>> {{attachment:headmodeler.gif}} {{attachment:openmeegOptions.gif}} 1. Explanations of the options: * '''BEM Layers & conductivities''': In this panel you can select how many layers you want to use for the BEM model. The possible options in our case are Scalp (=head), Skull (=outer skull), and Brain (=inner skull). The values on the right are the relative conductivities of each layer. * For EEG: Use all the layers * For MEG: Use only the inner skull layer * '''Use adjoint formulation''': Decrease significantly the amount of memory that is necessary in memory and on the hard drive, but much longer. * '''Use adaptive integration''': This produces a much more accurate solution, mostly in the cases of dipoles (vertices of the cortex surface) that are very close to the inner skull layer. You should keep this option selected. * '''Process dipoles by blocks''': If you consistently run into crashes, it's probably because you don't have enough memory available. You can try to process the dipoles by smaller blocks. It would be longer but would probably work. Do not select unless you cannot compute the solution with having memory errors. 1. Download OpenMEEG software? Yes.<<BR>> This will download the latest version of OpenMEEG binaries for your operating system from INRIA website, and install it in Brainstorm user folder (~username/.brainstorm/openmeeg/)<<BR>><<BR>> {{attachment:openmeegDownload.gif}} 1. Once downloaded, the calculation of the head model will start automatically. You may wait for a very long time. Be patient, it's worth it...<<BR>><<BR>> {{attachment:openmeegWait.gif}} 1. You have now a new head model in your condition, that you can use exactly the same way you would use your previous "Overlapping sphere" model.<<BR>><<BR>> {{attachment:treeFinal.gif}} |
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| It provides for EEG a much better forward solution than the previous "3-shell sphere" model. EEG users should try to switch to this method quickly. | == Additional discussions on the forum == Download problems: * [[http://neuroimage.usc.edu/forums/showthread.php?1066-Impossible-to-download-OpenMEEG|http://neuroimage.usc.edu/forums/showthread.php?1066]] Binary issues / Error #-1073741515: * [[http://neuroimage.usc.edu/forums/showthread.php?744-Problem-with-BST-and-Windows-7|http://neuroimage.usc.edu/forums/showthread.php?744]] * http://neuroimage.usc.edu/forums/showthread.php?767 * http://neuroimage.usc.edu/forums/showthread.php?1145 Library issues / Error #1: * http://neuroimage.usc.edu/forums/showthread.php?1309-compute-head-model-issue Memory allocation failed: * http://neuroimage.usc.edu/forums/showthread.php?1138 Intersecting meshes: * http://neuroimage.usc.edu/forums/showthread.php?1030 * http://neuroimage.usc.edu/forums/showthread.php?1305 Format of the Gain matrix in the headmodel file: * http://neuroimage.usc.edu/forums/showthread.php?918 * http://neuroimage.usc.edu/forums/showthread.php?1353 == License == OpenMEEG is distributed under the French opensource license [[http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html|CeCILL-B]]. It is intended to give users the freedom to modify and redistribute the software. It is therefore compatible with popular opensource licenses such as the GPL and BSD licenses. The CeCILL-B license imposes to anybody distributing a software incorporating OpenMEEG the obligation to give credits (by citing the appropriate publications), in order for all contributions to be properly identified and acknowledged. The references to be acknowledged are: * Gramfort, T. Papadopoulo, E. Olivi, M. Clerc. OpenMEEG: opensource software for quasistatic bioelectromagnetics, [[http://www.biomedical-engineering-online.com/content/9/1/45|BioMedical Engineering OnLine 45:9, 2010]] * Kybic J, Clerc M, Abboud T, Faugeras O, Keriven R, Papadopoulo T. A common formalism for the integral formulations of the forward EEG problem. [[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=30034&arnumber=1375158&count=10&index=1|IEEE Transactions on Medical Imaging, 24:12-28, 2005.]] [[ftp://ftp-sop.inria.fr/odyssee/Publications/2005/kybic-clerc-etal:05.pdf|[pdf]]] == Feedback == <<EmbedContent(http://neuroimage.usc.edu/brainstorm3_register/get_feedback.php?Tutorials/TutBem)>> |
OpenMEEG BEM head model
Authors: Francois Tadel, Alexandre Gramfort
This forward model uses a symmetric boundary element method (symmetric BEM) and was developed by the French public research institute INRIA (website). It uses three realistic layers (scalp, inner skull, outer skull). The goal of this forward solution is mostly for EEG users, to provide a better model than the existing "3-shell sphere". It is not necessary for MEG users, as the "overlapping spheres" method gives relatively similar results but faster. Nevertheless, for demonstration purpose or in case you want to use the same head model for both EEG and MEG data, we are going to compute this solution on MEG recordings, using the existing TutorialCTF protocol.
Contents
Requirements
On Windows 64bit systems, you need to install an extra Microsoft software package to run OpenMEEG: Microsoft Visual C++ 2010 Redistributable Package (x64).
http://www.microsoft.com/en-us/download/details.aspx?id=14632
BEM surfaces
We need three realistic layers extracted from the subject's MRI (scalp, inner skull, outer skull), plus the source space (cortical surface). Those layers are sometimes complicated to generate. In the case you do not have any way to calculate the inner skull and outer skull surfaces, Brainstorm can generate rough approximations based on the subject's cortex and head surfaces and Colin27's inner and outer skull surfaces.The surfaces created with Brainstorm are by construction non-intersecting.
- Select the TutorialCTF protocol
- Go to the anatomy view (first button on top of the database explorer)
Right-click on Subject01 > Generate BEM surfaces...You can set the approximate number of vertices you want for each layer. For the example, leave the default parameters and click on Ok.
Note that those values are very low and could lead to incoherent results. However, using more vertices on each layer can increase a lot the amount of memory necessary and the computation time. If you can afford it computationally, you should use a minimum of 2000 vertices per layer. Note that you may not get the number of vertices you are asking for, the algorithm generating those surfaces uses a fixed set of apolar spheres with the following number of vertices: 273, 362, 482, 642, 812, 1082, 1442, 1922, 2432, 2562, 3242, 4322...
![[ATTACH]](/moin_static198/brainstorm1/img/attach.png "[ATTACH]")
At the end of the process, three new surfaces are added to the database:
![[ATTACH]](/brainstorm/Tutorials/TutBem?action=AttachFile&do=upload_form&ticket=00676c5efd.a7530a3ad483a4d057d1ed28f5c9b40983e3975b&target=bemOptions.gif "[ATTACH]"){kind=small}
![[ATTACH]](/brainstorm/Tutorials/TutBem?action=AttachFile&do=upload_form&ticket=00676c5efd.a7530a3ad483a4d057d1ed28f5c9b40983e3975b&target=bemFiles.gif "[ATTACH]"){kind=small}
![[ATTACH]](/brainstorm/Tutorials/TutBem?action=AttachFile&do=upload_form&ticket=00676c5efd.a7530a3ad483a4d057d1ed28f5c9b40983e3975b&target=bem3d.gif "[ATTACH]"){kind=small}
Forward model
- Switch to the view "Functional data (sorted by subjects)"
Right-click on Subject01 / Right > Compute head model. Select OpenMEEG BEM in the list. Click on Run.
- Explanations of the options:
BEM Layers & conductivities: In this panel you can select how many layers you want to use for the BEM model. The possible options in our case are Scalp (=head), Skull (=outer skull), and Brain (=inner skull). The values on the right are the relative conductivities of each layer.
- For EEG: Use all the layers
- For MEG: Use only the inner skull layer
Use adjoint formulation: Decrease significantly the amount of memory that is necessary in memory and on the hard drive, but much longer.
Use adaptive integration: This produces a much more accurate solution, mostly in the cases of dipoles (vertices of the cortex surface) that are very close to the inner skull layer. You should keep this option selected.
Process dipoles by blocks: If you consistently run into crashes, it's probably because you don't have enough memory available. You can try to process the dipoles by smaller blocks. It would be longer but would probably work. Do not select unless you cannot compute the solution with having memory errors.
Download OpenMEEG software? Yes.
This will download the latest version of OpenMEEG binaries for your operating system from INRIA website, and install it in Brainstorm user folder (~username/.brainstorm/openmeeg/)
Once downloaded, the calculation of the head model will start automatically. You may wait for a very long time. Be patient, it's worth it...
You have now a new head model in your condition, that you can use exactly the same way you would use your previous "Overlapping sphere" model.
![[ATTACH]](/brainstorm/Tutorials/TutBem?action=AttachFile&do=upload_form&ticket=00676c5efd.a7530a3ad483a4d057d1ed28f5c9b40983e3975b&target=openmeegOptions.gif "[ATTACH]"){kind=small}
Additional discussions on the forum
Download problems:
Binary issues / Error #-1073741515:
Library issues / Error #1:
Memory allocation failed:
Intersecting meshes:
Format of the Gain matrix in the headmodel file:
License
OpenMEEG is distributed under the French opensource license CeCILL-B. It is intended to give users the freedom to modify and redistribute the software. It is therefore compatible with popular opensource licenses such as the GPL and BSD licenses. The CeCILL-B license imposes to anybody distributing a software incorporating OpenMEEG the obligation to give credits (by citing the appropriate publications), in order for all contributions to be properly identified and acknowledged.
The references to be acknowledged are:
Gramfort, T. Papadopoulo, E. Olivi, M. Clerc. OpenMEEG: opensource software for quasistatic bioelectromagnetics, BioMedical Engineering OnLine 45:9, 2010
Kybic J, Clerc M, Abboud T, Faugeras O, Keriven R, Papadopoulo T. A common formalism for the integral formulations of the forward EEG problem. IEEE Transactions on Medical Imaging, 24:12-28, 2005. [pdf]
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