Hello to everyone!
I am a student trying to compare various toolboxes and methods to solve the inverse problem. To do that my intention is to simulate a EEG from a signal in certain ROIs in the brain and then perform the inverse and evaluate.
In order to do that, I am trying to simulate the signal using the info in
Going a little bit to the detail i need the ROIs to correspond with the volumes of an Atlas, Desikan Killiani for example, and here is where I cannot figure it out. What i've been trying so far is from a MNI-based parcellations create an atlas in the scout tab, as mentioned in https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases but the scouts end up being surfaces.
I'm using the tutorial database for the anatomy and tried the process above both with the cortex of the default anatomy and on the bem model computed for a specific simulation.
I would really appreciate some help, I am new to brainstorm and despite doing the basic tutorials i lack fluidity to solve it. Thanks in advance.
To obtain a volume atlas, you must have volume source maps opened, otherwise the menus
Atlas > From subject anatomy would create a surface atlas.
This is because the volume source grids are saved in the headmodel and source results, not in the cortex surface.
Hi! Thanks for the quick response.
Yeah, tried that already and the exact same result. Attached you can find the capture with the volume source grid opend and the result from performing the
Atlas > From subject anatomy. May be that I'm confused and that is actually not the volume source map.
You need to have actual volume source results opened, not the source grid.
And I can't see any in your database, so you should start by simulating some.
Okay, that solved it. Thank you very much!
One further question on the matter, I cannot visualize the volume scouts despite them being created (i see the atlas and in the info that the scopes have a volume indeed). Also when i try to aply a signal to one of them in order to simulate source maps they are misplaced. For example, i had a signal that i applied to the Lateral Occipital R from Desikan Killiany atlas and appeared around the middle brain instead. Because i cannot see the volume atlas (i can with the surface ones) i don't really know whether if the scout is on the right place to begin with or not.
If you can't see the volume scouts, this is most likely because the 3D figure you are trying to use does not contain volume source results (the actual source maps, not the grid of points as you posted previously). Or the grid you used for creating the atlas is not the same as the one used in the displayed file.
If you can't understand what the problem is, please post screen captures showing: the file in the database explorer, the scout tab with the selected atlas, the 3D figure with the volume source results displayed on orthogonal MRI slices.
Hi! Yeah, the visualization problem was just that, opening the 3D figure of the source map and visualizing the scouts. Thanks a lot and sorry for the trouble, as I said I am completely new with the software and a bit clumsy still.
With the source activity simulation however, there seems to be a problem, I don't know if i am doing something wrong too. I generated a 3 component signal with matlab and imported it to BS, then in Process user matrix clicked on run, simulate, full source maps from scouts. Here i selected the scout where i wanted to apply the signal ( in this example the Lateral Occipital R from Desikan killiani atlas) and clicked on Run. Here is an image with the result, in blue the scout and as you can see, the activity from the MRI view is pretty far from it.
I think the problem is that your are using a volume scout defined on a grid that is not the same as the one used in the head model defined in your subject. Actually, from the files I see in your database, I don't understand how you managed to obtain these results.
I realized that there is no straightforward way to simulate data using volume head models, if you don't have any EEG data available in the first place.
I'd recommend you start with a surface model, much easier to work with, especially if you are want to use the Desikan-Killiany atlas, which is defined on the cortex surface, not in the volume.
If for some reason you really want to use a volume grid, here is how to proceed:
- Create a new subject
- Create a new sub-folder
- Right-click on the folder > Import channel file or Use default EEG cap
- Right-click on the folder > Compute head model > Cortex surface
- Right-click on the folder > Noise covariance > No noise modelling
- Run process "Simulate > Simulate generic signal" to create 3 signals, set correctly the subject and folder
- Select the simulated file in Process1, run process "Simulate > Simulate recordings from scouts", select any SURFACE scout - no need to select the option "Save sources", this is only to generate some EEG data.
- Right-click on the folder > Compute head model > MRI volume
- Right-click on the simulate EEG data > Compute sources > anything
- Right-click on the sources for the simulated EEG data > Cortical activates > Display on MRI (3D)
- In the Scout tab, menu Atlas > From subject anatomy > Desikan-Killiany
- Close the 3D figure
- In Process1, select the initial simulate signals (not the EEG), run process "Simulate > Full source maps from scouts", select atlas "Volume XXXXX: Desikan-Killiany", scout "Latera occipital R"
But again, I think it might be much easier for you to start with a surface source model.
I am currently working on a project involving source simulation and evaluation. I was trying to simulate two signals in two different volumetric scouts corresponding to the ROIs of Desikan Killiani atlas. The creation of the volumetric model, after some help from Francois, works perfectly but when i tried to perform the simulation the signals appear in many ROIs but the ones I intended to.
To test if the problem was mine i tried to do the simulations without noise or anything and see in wich ROIs the signal appeared. In the images you can se my current DB :
where s1&2 are the signals i intend to simulate at source level, "matrix" test is the concatenation of those signals for simulating both ROIs in one run; "recording" test is the EEG simulated from the previous matrix. So, the ROIs where i intended to put those signals are the Frontal Pole L and the Lateral Occipital R from Desikan Killiani atlas as i explained before. Follows the images of the volumetric scouts.
Now, when i use either the
Simulate recordings from scouts or
Full source maps from scouts the result is the same, the signals appear in scouts/ROIs that have nothing to do with the two that i select in the menu. In the picture you can see both the activity sourcemap and the signals from
scouts time series related to the simulated source map.
So, according to what i could understand from the tutorials, these functions put the signals in all the vertices contained within the volumetric scopes and zero in the others (i am not adding noise in any step) but the activity maps and the signals at scope level show otherwise. I have also checked that the scouts are in the ritght place just in case the location was somehow wrong.
Pardon the weird view but was the only way to show both.
I moved this other post here, as I think I already addressed it.
Hi! Thanks a lot, generating the volume scouts from sources that were calculated instead of simulated did the trick. The volume approach comes from my tutor in the project, she wants to be ablo to have deep brain structures so... Anyway, thanks again for the help, Have a great weekend!