Hello,
I would like to solve inverse problem (source reconstruction) via the software over whole time series (resting-state) for whole brain including cortex and sub-cortical regions. Is it possible to generate whole brain regions/vertex for M/EEG full time series?
Thanks you,
Hi Sshams,
Brainstorm can do this. You can make a source space encompassing the whole brain volume or specific volumes. This tutorial explains how to make a full volume source space and solve the inverse problem for that with volume scouts.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource
Kind regards,
Steven
Hi Steven,
Thank you very much for your response. When I used "Compute Source", I got the error "Error: No noise covariance matrix available.". How can I produce it. I only have one subject for analysis?
Cheers,
Saleh
Thank you
Hi Saleh,
Indeed for techniques like sLORETA you will need a noise covariance matrix to take into account the correlation between sensors. The following brainstorm page will give you more information about how to produce it : https://neuroimage.usc.edu/brainstorm/Tutorials/NoiseCovariance
Kind regards,
Steven
Dear Steven,
Thank you very much. I produced the covariance matrix and then computed the sources as it explained in the manual. I would like to extract all the time series corresponding to the vertexes located in each region (cortex and structures) and export to the MATLAB for further analysis. Would you please explain to me how to do that?
Best regards,
Saleh
Dear Saleh,
You can export your source localization results to matlab by clicking right clicking on the results and then via file -> export to matlab. That will give you a struct with in it a matrix called ImageGridAmp which gives the time series for each vertex.
You could also use volume scouts if you want just a few source time series, but that is up to you.
Kind regards,
Steven
I would like to solve inverse problem (source reconstruction) via the software over whole time series (resting-state)
For the analysis of resting-state recordings in source domain, you can refer to the following tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega
I would like to extract all the time series corresponding to the vertexes located in each region (cortex and structures) and export to the MATLAB for further analysis
You can use the process "Extract > Extract time series". It would produce .mat files that you can directly load in Matlab with the signals of interest.
If you want the averaged time series for the scout, select the scout function "Mean". If you want the signals associated to each source individually, select "All".
https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#Scout_function
If you are planning to process Brainstorm files outside of Brainstorm, this tutorial page contains all the information you need.
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Reference:_File_manipulation
Great, thank you very much!
Hello Francois,
I followed the resting-state manuals, and I tried to produce the time series of scouts. Unfortunately, this message appeared: "NO AVAILABLE SOURCE FILES", while I computed the sources according to the instruction before (please see the below link to the screen shot). Thank you!
The screen capture you posted does not show any error, I can't see anything wrong with it.
If you get an error, please tell us exactly how you get to this error from the interface, and copy-paste here the full error message from the Matlab command window.
Thanks
Thank you for your response. I load the aseg atlas for scout. Next, I set the suction to PCA (and All). An then tried to see (export) the time series. I used the "scout Time Series" in cortical activation> scout time series (first link), and by clicking on the second button in the toolbar [Display scouts time series] (second link). Both of them results in the error I have attached to the below links.
Here is the full error message from the Matlab command window.
BST> Error: Cannot use a surface scout to extract value from a volume grid.
BST> Error: Cannot use a surface scout to extract value from a volume grid.
I do not know what I am missing! Thank you
The problem is indicated in the error message: "Cannot use a surface scout to extract value from a volume grid."
You loaded your atlas as a surface atlas on the cortex surface. The result is an Atlas where each scout is a subset of some vertices of the cortex surface.
However, you computed a volume source model: the source space (= the dipoles for which the activity was estimated) is not the cortex surface, but a grid of points sampling the full head volume. There can't be any correspondence made between your dSPM sources estimated on this volume grid and the surface scouts you see in the Scouts tab.
You need either to load the ASEG atlas as a volume atlas (display the dSPM sources, then in the Scout tab, menu Atlas>Load atlas> File format "Volume mask or atlas (no overlap, subject space)")
or compute surface-based sources.
Thank you very much Francois! Is there any volume atlas in the freesurfer anatomy file, if not, how can I generate it? And, how can I compute surface-based source?
Dear Francois
Thanks to your explanation. I used aseg.mgz instead of aseg+aparc from the anatomical folder, and the previous problem was solved.
Cheers