Hi Conn gurus:

I want to run two full analyses (through second level) trying out both the intermediate and conservative scrubbing parameters offered in the preprocessing pipeline (using art). I was prepared to setup two different .mat files with their associated folders in order to run scrubbing and the remaining steps separately and in parallel. But it occurs to me now that the scrubbing procedures work by creating new art-related files directly in the subject functional data folder, and if I first run scrubbing with one threshold (e.g. intermediate) and proceed with analysis, and then move to a different .mat file to run a new threshold (e.g. conservative), this will overwrite the art files in the subject's functional folder and thus may interfere with the first (e.g. intermediate threshold) analysis being run.
To your knowledge is there any solution other than creating two copies of my subject functional folders in order to use one copy for one scrubbing setup and the other for the other scrubbing setup?

Thanks for any advice!
Emily