Hi Rick,

Thanks so much for all of your helpful responses! Just wanted to check in on a few final things (sorry). I only have one run, so I deleted the "-regress_ROI_PC_per_run" line. Just wanted to confirm that that's correct.

For the "-regress_ROI_RC" line, I used 3 as the number of principal components because that's the number used in the example. Is there a better justification for selecting the first 3 PCs vs. some other number?

Lastly, it's taking about 8 hours per subject to run. Is this to be expected? I chose 11b over 11 because I thought it might be a bit faster to skip Freesurfer, but I wanted to regress out WMe and CSFe restricted to the ventricles. Is there a way to add something to take advantage of parallel processing (like -jobs in the 3dD options)?

Thanks!
Laura