Differences between revisions 7 and 12 (spanning 5 versions)

OpenMEEG BEM head model

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 very similar results but much faster. Nevertheless, for demonstration purpose, we are going to compute this solution on MEG recordings, using the existing TutorialCTF protocol.

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 > Compute BEM surfaces...You can set the approximate number of vertices you want for each layer. Leave the default parameters and click on Ok.
At the end of the process, three new surfaces are added to the in the database:

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 adaptative 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 much 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.

-  ⇤ ← Revision 7 as of 2011-05-15 03:45:23 → 
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  Editor: cpe-76-169-10-66
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+   ← Revision 12 as of 2011-05-15 06:10:04 → ⇥
  Size: 3772
  Editor: cpe-76-169-10-66
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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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, using the existing TutorialCTF protocol.
+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, using the existing TutorialCTF protocol.
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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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-. Right-click on Subject01 > Generate BEM surfaces...
+. Right-click on Subject01 > Compute BEM surfaces...You can set the approximate number of vertices you want for each layer. Leave the default parameters and click on Ok.<<BR>><<BR>> {{attachment:bemPopup.gif}} {{attachment:bemOptions.gif}}
 1. At the end of the process, three new surfaces are added to the in the database:<<BR>><<BR>> {{attachment:bemFiles.gif}} {{attachment:bem3d.gif}}
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+Line 16:
-. Right-click on Subject01 / Right > Compute head model. Select OpenMEEG BEM in the list.
 1. Click on Run

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.
+. 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 adaptative 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 much 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>>

Software

Users

Development

OpenMEEG BEM head model

BEM surfaces

Forward model