Hi,

in the fcon-1000 preprocessing scripts it is not possible to add motion-related spike regressors (if you know what you're doing it is possible to implement it by hacking the 5_nuisance.sh script). In addition, I'd like to remind that the fcon-1000 scripts are no longer supported, and are actually a bit outdated when it comes to resting state fmri preprocessing. A good alternative would be to look at CPAC at http://fcp-indi.github.io/

hth,
Maarten