Issue in the reconstruction of brain volume sources

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1

Dear users,
I am trying to obtain time series after having reconstructed suorces in the whole brain. To do so I ve tried two different approaches. In the First approach, I have:
1-computed a 3D head model by choosing 'Source Space' -> MRI volume, keeping all the following OperMEEG options at the default values
2-reconstructed sources through sLoreta.

However, when I upload atlases with volume scouts such as AAL or ASEG from Free Surfer, it seems that Brainstorm interprates each scout of these atlases as surfaces instead of as volumes since I get each time the error (on matlab) "Error: Cannot use a surface scout to extract value from a volume grid. "

Can you explain me why?

with this approach, of course, I cannot finally find time series belonging to the scouts

Second Approach: I have:
1-computed a head model by choosing 'Source Space' -> Cortez Surface, keeping all the following OperMEEG options at the default values
2-reconstructing sources through sLoreta.

In this case, when I upload atlases with volume scouts such as AAL or ASEG from Free Surfer i manage to find time series in cortical regions. However, how is it possible that I have time series belonging to sub-cortical regions even if my source space in the head model is the cortex surface?

Hope to find a solution..i am struggling quite a lot with these issues

2

You are maybe doing something wrong. I just tested that if you do the following, you would get a volume atlas and you would be able to get time series for each ROI.

  1. Compute a volume head model and estimate sources from it
  2. Right-click on the source file > Cortical activation > Display on MRI (3D)
  3. Scout tab > Menu Atlas > Load atlas > File format: Volume mask or atlas (xx, subject space), File: aseg.mgz
    https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases

Second Approach: I have:
1-computed a head model by choosing 'Source Space' -> Cortez Surface, keeping all the following OperMEEG options at the default values
2-reconstructing sources through sLoreta.

In this case, when I upload atlases with volume scouts such as AAL or ASEG from Free Surfer i manage to find time series in cortical regions. However, how is it possible that I have time series belonging to sub-cortical regions even if my source space in the head model is the cortex surface?

AAL and ASEG are volume atlases, they should not be used for surface source models.
Use the surface-based atlases available when importing FreeSurfer subject folders in Brainstorm.
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Cortical_parcellations

3

Dear Francois, Thanks a lot for your prompt response. I have to punctualize that I am working with EEG data (missing info in my previous message).
Regarding the first approach (source reconstrunction after the creation of a 3D-head model) I followed the tutorial. However, only today I have finally menaged to find time series belonging to 3D volumes by using Overlapping spheres method instead of OpenMEEG BEM (which is recommended for EEG signals processing and was previously used in my not-working analysis). Can you explain me why?
I thank you again for your help and Support

4

only today I have finally menaged to find time series belonging to 3D volumes by using Overlapping spheres method instead of OpenMEEG BEM (which is recommended for EEG signals processing and was previously used in my not-working analysis). Can you explain me why?

The choice of forward model has no impact on the options you have for estimating sources.
There is something else you've done differently.
I recommend you start over and check step by step carefully what you're doing.