Hi Rick,
Thanks for your reply to this, and sorry it took me so long to write back; I was out of the country for a bit after I sent my initial inquiry.
Your initial thought was correct, creating stimulus timing files for this particular project is going to be quite involved and I would like to not have to do it needlessly for subjects that will have to be thrown out anyway. I believe that the easiest thing would be, as you suggest, to just run preprocessing partially once, check the data and then delete the results/re-run after determining which subjects, if any, are not going to be usable based on technical issues with the scanner equipment during data collection.
Thank you for your suggestions.
Best,
Dominic