Thank you for your reply. We agree that the order of operation between censoring and de-meaning of the baseline columns of the design matrix may have little impact on the population data.

For us to properly evaluate this order of operations, we have a few remaining questions:

1) Is there a built in option in 3Ddeconvolve or another suggested operation to perform the censoring before de-meaning of the baseline columns?
What's your advice on using 1dtool.py to apply the censoring before creating the design matrix xmat file using 3Ddeconvolve?
2) Is there a reason that 3Ddeconvolvelocks in the order of operation to de-mean then censor that we should consider before switching the order?

Thanks again.