Simulate sources using brain template and CTF-275

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1

Hi,

I would like to simulate what scalp topography I would get given a specific dipole location in the brain.

In other words, assuming a given MNI coordinate, a given dipole orientation, what would the scalp topography look like?

For the analysis, I would like to use (1) a brain template provided with Brainstorm and (2) for the location of the channels some sort of default for CTF 275 if anything like that exists.

I’ve spent a while looking around the tutorials, but could not find much.

I am not an advanced user, so if anyone finds the time to reply I would be grateful if the response could not assume too much prior knowledge on my side :slight_smile:

Thanks a lot in advance!

2

Hello,

There is not much in the tutorial pages, but lots of information on this forum. You can search it for “simulate” or “simulation” to find many examples.

You procedure is the following:

  1. Define some source activity, with the process "Simulate > Simulate generic signal"
    http://neuroimage.usc.edu/brainstorm/Tutorials/TimeFrequency#Simulation
  2. Create a scout to which you want to set this activity (you can use the menu “Scout > New: Coordinates” to create a new ROI based on MNI coordinates)
    http://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#Scout_toolbar_and_menus
  3. Associate the signal with the cortex patch and use this to simulate EEG or MEG recordings, with process “Simulate > Simulate recordings from scouts” (select the simulated signal in Process1, and select the scout in the process options)

Alternatively, you can create your own source matrix and then use the menu “Model evaluation > Simulate recordings”:

  1. Compute some random source results in Brainstorm with the option “Full sources”
  2. Export it to Matlab and replace the field “ImageGridAmp” with your own data. If you change the number of “time points” (second dimension of the matrix), you must update the field .Time as well (length(Time) must be equal to size(ImageGridAmp,2))
  3. Change the .Comment field as well, to identify the file in the database.
  4. Right-click on the folder > File > Import from Matlab, to import your modified structure
  5. Simulate recordings: http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Model_evaluation

Cheers,
Francois

3

Thanks a lot for your reply.

I got to the last point, but Brainstorm is asking me for a channel file. Is there a default channel file I could load rather than one of a specific subject? I am using CTF-275.

4

You can simply use the channel file from one of the runs in the introduction tutorials (copy-paste it where you need).
The MEG recordings were collected with the CTF-275 system at McGill.

If you haven’t followed the introduction tutorials yet, I would recommend you start by reading all the pages in the “Get started” section.
http://neuroimage.usc.edu/brainstorm/Tutorials

Francois

5

Thanks again. Maybe this is a misunderstanding on my side, but I was assuming that each Channel file was referenced to the fiducial markers, whereas I would like some channel file that is kind of general (essentially assuming the template head was in the MEG, like a template Channel file). I know there is no unique solution, but I thought there might be some sort of default. If my assumption is incorrect, then I can essentially just use any subject, right?

6

The channel file is registered on the MRI using the anatomical landmarks NAS/LPA/RPA. This describes the relative position of the head in the MEG.
If you’re running simulations, you need to decide where to put the subject in the MEG arbitrarily… you can edit this registration manually: right-click on the channel file > MRI registration > Edit.

7

Ok, thanks. This is what I did and the results look reasonable. Just thought there perhaps was something like a generally-accepted default position.

Thanks again for your help!

8

FYI: To address all the recent questions we had related with simulations, I added some code in Brainstorm and wrote a new tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations

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