I think my description of PESTICA is confusing, so I'll summarize.  PESTICA requires the temporal information, so the -d option should be the 3D+time dataset.  If you use the skull stripped brain as input, the ICA won't run as there will be no temporal data.  The first three stages of PESTICA are estimation steps that result in two vectors matched to your 3D+time dataset input, these should match up with a parallel monitored pulse oximetry and respiratory bellows signals.  The PESTICA algorithm produces these signals for you when you don't have a pulse ox or respiration measurement built into your pulse sequence or it failed during the scan.  Then you can use these estimators (when everything works right and these would match up with pulse ox/respiration its perhaps not appropriate to call them estimators, they're more "derived pulse trace and respiration trace" signals) in any of the other pulse ox/respiration signal correction methods, such as RETROICOR.  Steps 4-5 of run_pestica.sh actually run RETROICOR (if you specify the -r flag) and IRF-RETROICOR, and 6 produces QA plots.  If you have pulse ox and respiration signals for each scan, then its better to use those.  We created PESTICA specifically because many sites don't have pulse ox/respiration in their pulse sequences.  Does that make sense?
erik