I was now wondering if it is possible to run "Extract scout time series" multiple times after each other, each time extracting a few scouts. In the process editor I see that I can't place multiple "Extract scout time series" options after each other. So I think making a script would be best right? Or is there a logical reason why "Extract scout time series" can't be used multiple times?
There is no reason for not calling multiple times the process "Extract scouts time series", but this would be terribly inefficient: it would load all the data, the inverse kernel, multiply the two to reconstruct this gigantic source matrix (Nsources x Ntime) in memory, and then average a few sources to get the scout time series. If you call twice the process, all this is done twice...
To optimize the memory and CPU usage of your scripts: learn how to use the resource monitor of your operating system, and the Matlab Profiler.
Why do you need all the time points loaded at once?
The most logical, if you want to split the process in two for memory reasons, would be to split the data along the time dimension. You need continuous signals at the end, you can concatenate the scout signals easily with a process.
I copied the first "extract scout time series" and adjusted the names of the two scouts that should be extracted.
Any idea why it is happening and how I can solve it?
You are erasing the variable with the original input filenames....
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Simplify_the_calls