You are using output=1, which corresponds to "Kernel only: shared" in the options of the process.
Brainstorm creates one shared inversion kernel every time you call the process "Compute sources". Each shared kernel is linked to each data file in the folder.
Some recommendations:
- Follow carefully all the introduction tutorials using the example tutorials before trying to script your analysis on your own data. This is all explained in there:
https://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Computing_sources_for_single_trials - Regenerate your script calls instead of using existing (and probably outdated) scripts. If you had done this, you would have had the comment
'output', 1, ... % Kernel only: sharedin the script, which could have helped you understand what was going on. - Compute only one kernel for all your files, you have no reason to compute the inverse model multiple times.
- Use a correct noise covariance matrix