Dear All,
I am quite new to Brainstorm and I apologize if this is a simple question or already were answered that I couldn’t find.
I am trying to run a connectivity analysis via my custom developed Matlab code on the sources that I have extracted via Brainstorm. However when it comes to visualize the sources, it becomes a bit difficult for me to understand where each sources located in. Although Brainstorm gives us the coordinates of the each source in GridLoc, I wonder is there a way to see in Brainstorm in which scout each source fell in? I mean is there a Brainstorm function that helps to visualize a source or number of sources?
Thank you very much for any comment or help,
regards
Hello,
Could you describe better what you are trying to do?
What type of data do you have (describe the structure, give an example) and what would you like Brainstorm to do with it?
You can add screen captures if it makes it easier to understand.
The data structures for the source files are available here:
http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#On_the_hard_drive
If you have a few signals available in the database (saved a “matrix” files), you can run the process “Simulate > Simulate recordings from scout”:
http://neuroimage.usc.edu/brainstorm/Tutorials/Statistics#Convert_statistic_results_to_regular_files
Cheers,
Francois
Hi Francois,
First of all thank you for getting back to me. I will try to explain what I aim to do. I have an EEG data collected on a visual object processing task, in which I have 360 trials each is 600 ms long. I used the default settings of Brainstorm which were recommended/used via the Source estimation tutorial on sample data. I mean I used wMNE as my method, Current Density map as my measure and constrained version as my source model. Hence I estimated 15002 sources per trial.
After that point I would like establish a connectivity map among the sources or cluster of sources via a custom Matlab code, using Phase locking value as the metric to observe phase synchrony between the sources. Due to my paradigm is language specific, I have interested several areas which are most important for me. Having 15002 sources, makes the analysis very costly and I would like to know which of these sources stays in the scouts that I am interested in. I know there is a coordinate file that gives the position information of the each source, but I am not sure how I will choose the sources that I am mostly interested in. Therefore I thought visualization of the each source in the 3D head or MRI viewer would helpful for me to extract those sources that I am mostly interested in and I wanted to ask if Brainstorm has that sort of visualization function or feature to see each individual source. I added my file structure for a single trial.
Again I would like to apologize if my question is in somewhere in the tutorials or in the forum and I missed that. I would really appreciate your help or pointing any source that you think would help to me.
Regards
Lisa
The summary is:
- you have a scout defined (ROI on the surface)
- you want to know for each vertex included in this scout what is the index of this source in the ImageGridAmp (or ImagingKernel) matrix
Correct?
The scouts are saved in the cortex surface file and documented here:
http://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#On_the_hard_drive
The list of indices of the sources in this scout is in the the field .Vertices
You can also access them directly in your Matlab workspace with the menu Scout > Export to Matlab:
http://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#Scout_toolbar_and_menus
If you load manually your source files, load their “full” versions with in_bst_results:
http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#On_the_hard_drive
Does this answer your question?
[QUOTE=Francois;10100]One last thing you can do is using the “Coordinates” tab:
http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#Get_coordinates[/QUOTE]
Dear Francois,
these are exactly what I needed at the moment. Thank you very much indeed.
Kind regards,
Dear Francois,
may I ask for another help it is possible please that, is there any chance to know coordinate of a ROI/scout’s itself from Brainstorm? Why I am asking, these ROI will be the nodes in the connectivity analysis to visualize the connectivity between the nodes I will need the rough coordinates. Or I would be very pleased if you could share if there is any method to visualize the connectivity among them please?
Thank you
Hi Lisa,
With the information I gave you previously, you can get the index of each vertex included in the scout (iVert = sScout.Vertices).
These indices correspond to the .Vertices field in the cortex surface.
Export the cortex surface to your Matlab workspace or load it in a script, and you will have access to the 3D positions of the points included in your scout (sCortex.Vertices(iVert,:)).
To get only one position for the scout, you can probably average these 3D positions: mean(sCortex.Vertices(iVert,:))
To render the connectivity matrices, you can use the graph display in Brainstorm (not documented yet…)
Compute any [NxN] connectivity metric on scouts, then right-click on the file > Display as graph.
You can compute your own connectivity matrices and import them as connectivity files in Brainstorm and display them this way.
Francois
1 Like
Dear Francois thank you very much again for very rapid help, it is helpful.
In the output files, the indices of the vertices in a scout are stored in the Atlas variable but the coordinates are stored in the headmodel_surf_openmeeg file, in a variable called GridLoc. There is another variable as well called GridOrient but I assume this gives the orientation of the dipole in a particular vertex isn’t it?
I haven’t tried importing my connectivity file to Brainstorm but I will try it soon then.
Thank you