Hi,

Your scripts continue to work well for me (I'm running a big batch of subjects as I write). The one part of the analysis pathway that it not crystal clear to me is the nuisance signal regression step. My problem is that I am an AFNI user and the main work of regressing out the nuisance variables is done using FSL programs. It appears that you are savvy in both AFNI and FSL, so I wondered why you preferred to use FSL for this part of the pathway? Would it work just as well to use 3dREMLfit in AFNI with the global.1D, csf.1D, wm.1D, and motion parameters as regressors and then write out the residuals?

My other question is whether you think that your pathway would also work for analysis of multiple resting epochs (20-30secs each) within the context of a task? Could one simply include a task-related EV in the model and proceed as usual otherwise? Or could one ignore the task epochs by using a -censor option within 3dREMLfit or 3dDeconvolve (don't know if a similar option exists for FSL)? I would appreciate your thoughts about this.

Lisa