Hi Andrew,
Note that the -*opts_* options in afni_proc.py (like your -regress_opts_3dD, which contains -GOFORIT) are for passing options that are unprocessed by afni_proc.py directly to sub-programs. That is to say, afni_proc.py does not know that you passed -GOFORIT to 3dDeconvolve. So since you are also running 3dREMLfit, -GOFORIT needs to be passed along there, too.
On the filp side, it would probably make sense for that option to be automatically passed along by 3dDeconvolve. But as it stands, that is not done.
So for now, add "-regress_opts_reml -GOFORIT" to the afni_proc.py command.
- rick
