I was looking at my output and it seems that when I use IM AFNI runs 3dREMLfit. I did not notice this when using -help for 3dDeconvolve and I can’t find 3dREMLfit in the tcsh, generated by the afni proc, that was used for my preprocessing pipeline. Should I assume that when using IM afni employs 3dREMLfit by default?
No, I think you are just seeing the output from
3dDeconvolve telling you how to run 3dREMLfit.
Unless you specify -regress_reml_exec and
-regress_3dD_stop, 3dDeconvolve will run.
Great thanks for clearing that up