Hi Rick:

I'm so sorry for my omission - yes, when I say .nii file I mean a 3d+time - 236-TR length - file with a potentially different regressor at every voxel. I was actually just looking at 3dTproject when I saw your message and it looks like I can use my file with the -dsort option. From my quick command check it seems like it gives a 3d+time - 236-sub-brik output file which is what I'm looking for.

In response to your second question: I am replicating a processing stream from a Tambini & Davachi (2013) paper where the .nii file I'm speaking of is a conglomerate WM & CSF ROI on which PCA is run. After PCA and the related temporal projections are complete, this 'nuisance' file is the only thing regressed from the time series (of both resting state and acquisition scans) which is why my thinking was a command as simple as '3dTproject -input XXX+orig -prefix YYY -dsort nuisance+orig'
As an aside, after this step the hippocampus is masked out and 'outlier' voxels are removed but I did think when I first read it that it was weird that not more (i.e. motion parameters) had been regressed out.

I hope that command looks kosher. This SEEMS to do what I'm looking for but right now I'm simply going by the fact that I get the right kind (read. length) output and will not know for sure until I try it tomorrow.

Thanks so much for your insight.

Lauren