Open MEEG BEM on Colin27

Discussions
1

I think I may have done something inappropriate with regards to generating my subjects head models. I neglected to not do the first 5 steps listed here: http://neuroimage.usc.edu/brainstorm/Tutorials/TutBem?highlight=(adaptive)|(integration) on Colin27, but have already created my BEM surfaces for my subjects using Open MEEG. I’m assuming that Open MEEG used the default ‘outerskull’ and ‘innerskull’ vertices to do this?

Should I instead have right clicked (default anatomy)> Generate BEM surfaces, change all fields to 2000, and then generate head models for each subject using the BEM surfaces generated from this (bem_head, bem_outerskull, bem_innerskull)? Also, after these surfaces are created they are appended with _1922V despite me specifying 2000 as suggested in the tutorial.

Ah yes, I now see that after doing those first 5 steps, they have been marked as the default files and in the head model window for each subject the vertices have been updated to 1922 (still unsure why this is not 2000). Perhaps I have answered this myself…and am in for a long day of Open EEG BEM processing…

  • Edit1: Currently, cortex_15002V is designated as the default. Do I want to designate cortex_330117V as the default? Or is this just a higher quality cortex to project sources? It goes much slower and is impossible to rotate smoothly when _330117V is selected

  • Edit2: I attempted to right click my subject node to run Open MEEG BEM for all my subjects, and after some time the process just stopped. No error messages and no output. I did notice that for my first subject, it was no longer using the default anatomy for some reason in the anatomy tab (perhaps I deleted it somehow). I’m assuming this would confuse Open MEEG, being told to run 16 subjects for which one does not have an anatomy? In any case, I couldn’t figure out how to re-link the subject to the default anatomy, so rather than it saying (default anatomy) under the subject node, I re-imported the Colin27 template for this specific subject. I hope this is fine!

Any clarification would be great, thanks!

2

Hello,

I neglected to not do the first 5 steps listed here: http://neuroimage.usc.edu/brainstorm...integration) on Colin27, but have already created my BEM surfaces for my subjects using Open MEEG. I'm assuming that Open MEEG used the default 'outerskull' and 'innerskull' vertices to do this?

I'm not sure I understand what you did. You are not supposed to run this "Generate BEM surfaces" on the default anatomy, the innerskull/outerskull surfaces already exist.
If you are using the default anatomy, you have nothing else to do before running the OpenMEEG BEM head model computation. If you are using the individual subjects MRIs, you need to run "Generate BEM surfaces" for each subject, after importing the result of the anatomical segmentation.

Also, after these surfaces are created they are appended with _1922V despite me specifying 2000 as suggested in the tutorial.

I added a comment to explain this in the tutorial:
"In output, you will probably not get the number of vertices you are asked 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..."

Currently, cortex_15002V is designated as the default. Do I want to designate cortex_330117V as the default?

The surface with 300000 vertices is what is generated by FreeSurfer, nice looking but too big for source reconstruction and visualization.
15000V is usually a good compromise between accuracy and usability, this is our recommendation. If you want to work with a number of sources in between, downsample the 300000V surface.

  • Edit2: I attempted to right click my subject node to run Open MEEG BEM for all my subjects, and after some time the process just stopped. No error messages and no output. I did notice that for my first subject, it was no longer using the default anatomy for some reason in the anatomy tab (perhaps I deleted it somehow). I'm assuming this would confuse Open MEEG, being told to run 16 subjects for which one does not have an anatomy? In any case, I couldn't figure out how to re-link the subject to the default anatomy, so rather than it saying (default anatomy) under the subject node, I re-imported the Colin27 template for this specific subject. I hope this is fine!

If you have a mix of different subject configurations (with and without individual anatomy), you cannot run the head model computation for all the subjects at once.
To change the configuration of a subject: double-click on the subject node and change the selection for the "Default anatomy" option.

Note that in the following conditions:

  • you are working with EEG,
  • you use the default anatomy for all the subjects
  • you use the same a default set of electrodes positions for all the subjects
  • there are no SSP projectors calculated on your recordings
    => you don't need to re-calculate the head model for each subject, compute it once and copy-paste it to the other subjects.

Cheers,
Francois

3

[QUOTE=Francois;6817]
If you are using the default anatomy, you have nothing else to do before running the OpenMEEG BEM head model computation.
[/QUOTE]

I’m not sure I’m clear on this point. In the Open MEEG BEM tutorial (http://neuroimage.usc.edu/brainstorm/Tutorials/TutBem), it says:

“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 [B][I]could lead to incoherent results[/I][/B]. 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 [B]2000[/B] vertices per layer.”

The default anatomy (Colin27), does not provide nearly 2000 vertices, and seemingly the only way to change the amount is by specifying during the Generate BEM surfaces step.

4

I edited the text in this tutorial.
Let me know if you still more explanations:

[B]How to set the number of vertices per layer[/B]
[ul]
[li]The more vertices you have for each layer, the more accurate your head model will be. If there are not enough vertices, OpenMEEG may consider that the surfaces are intersecting and crash before the computation, or it may finish but at the end the model may be instable with a few vertices with values much higher than all the others.
[/li][li]On the other hand, using more vertices on each layer increases a lot the amount of memory necessary and the computation time. If your system hangs, if it takes 24hrs to run or if you get “Out of memory” errors, you have to decrease the number of vertices for each layer.
[/li][li]The default values are high (1922 vertices per layer), to ensure that by default the results are good. If you can afford it computationally, you should use those 1922 vertices per layer. If you have to decrease those values, you can try for instance with 1082 vertices (scalp) and 642 vertices (outer skull and innser skull).
[/li][li]In output, you will probably not get the number of vertices you are asked 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…
[/li][li]If you are using the default Colin27 anatomy, you do not need to run this, you can directly use the head/outerskull/innerskull surfaces in the the default anatomy folder. The number of vertices is much lower, but we know this anatomy to be stable, you should not need to recalculate new surfaces with more vertices.
[/li][/ul]

5

[QUOTE=Francois;6830]
you should not need to recalculate new surfaces with more vertices.
[/QUOTE]

Just to drive this point point home, should I now delete the head model I created after generating BEM surfaces from the default, and just use the default head/outerskull/innerskull? Or can I continue using the head model I created after generating 1922 vertices from the default. Specifically, is what I did unnecessary but not problematic…or is recalculating new surfaces with more vertices from the default going to give me incoherent results?

6

If you have calculated new BEM surfaces in the default anatomy (Colin27), I would recommend you delete them and just use the ones that were there initially.
If you’re not sure what you’ve done, to reset to the default template: Right-click on (Default anatomy) > Use template > Colin27