I am working with volume scouts and MEG recordings. I can easily extract the scouts time series. However, I would also like to extract the scouts coordinates. If I got it right, when I extract the scouts time series I also get some integer numbers (under exportedStruct.Atlas.Scouts.Vertices) identifying the vertices.
I have tried to use two different approaches to get the corresponding coordinates.
I exported the source-reconstructed file [MN: MEG(Unconstr) 2016] to matlab, and extracted the locations from sourceStruct.GridLoc(#vertex). However, the coordinates that I obtain do not match those declared by Brainstorm in the MRI view, when I center the view on a scout.
I exported the cortex file [cortex_8004V] to matlab, and and extracted the locations from cortexStruct.Vertices(#vertex). In this case, the obtained coordinates do match those declared in the MRI view for a given scout, but only if the scout has a single vertex. If the scouts has more than one vertex, and thus a list of #vertex integers, only the “seed” vertex returns the matching coordinates, while the other ones do not. I created a scout with 15 vertices by enlarging it, and all vertices appear to be very close to each other in the MRI 3D view, but once I export everything and I try to get back the coordinates as I just described, I find the vertices to be at seemingly random positions within the brain.
What am I doing wrong?
Thank you for your kind attention.
Cheers,
Alessio Perinelli
What kind of source model is it?
What options did you use for the head model and source estimation?
If you have a non-empty field “GridLoc” in the source file, I guess you are using a volume head model. If this is the case, you are not using the cortex as the source model, there is no point in trying to get the coordinates of the scouts from the cortex surface, you can only get the positions from the head model or the source results.
Some more description of your issue would help, maybe a screen capture, or the contents of your various structures.
I'm interested in extracting the [x y z] coordinates of my atlas scouts.
To answer the questions above, I have computed a volume head model and performed unconstrained MN source estimation using sLORETTA as measure.
I tried to extract these 3 coordinates from multiple data structures. If I choose the option 'Save selected scouts to file', I get the scouts' seed as a 1D vector:
And if I extract my Source file, I get the 3 coordinates of the grid, but I don't really know how to use them to extract the 3 coordinates of my scouts.
Please, does anyone have suggestions on how to proceed?
Edit: I also saw this post: Seed mni coordinates and I am still having difficulties. When I am asked to apply the cs_convert function, I am asked to feed to it a list of points in [Npoints x 3] format:
