To remove the global mean from a .1D file, something like this would work:
3dDetrend -DAFNI_1D_TRANOUT=YES -prefix - -polort 0 fred.1D\' > defred.1D
Note the backslash+single-quote combo at the end of the filename -- this is very important.
The rationale for removing the mean from the global regressor is simply to make the 3dDeconvolve matrix more stable -- so that the matrix doesn't have 2 columns that are virtually the same. Mathematically, in infinite precision arithmetic, this would be unneeded.