So my new computer is a mac (old machine Linux) and I tested an AFNI proc script I used on my old computer and it worked fine. Looking back at the tcsh script I noticed something strange under 3dDeconvolve I can’t find stim file for the motion regressors but they are present in the tcsh script produced by the same AFNI proc options on my old computer. It still seems to be conducting motion regression under 3dDeconvolve -ortvec motion_demean.1D mot_demean appears above the -polort option. Is ortvec a new default? I have generated other scripts (different AFNI proc options) and I don’t get motion stim file but rather ortvec.
Thanks for your input
Yes, the motion regressors are now being applied via -ortvec. They will have the same effect, it is just a more compact notation that requires only 1 simple option, rather than 6 messier ones.
You should be able to compare the regression matrices to see that they are basically the same (there might be a registration difference though).
Great thanks for clearing this up. Also, lets say I wanted to run a regression on 4 out of my 6 runs I assume it is fine to use the motion_XXX_censor.1D and motion_demean.1D files? They will be longer than needed but I assume AFNI will simply not use the extra numbers.
That would be okay, as long as those are the first 4 out of 6 runs. Otherwise, they would need to be adjusted.
It is the first four out of the 6, I will look at the first one on its own then the first and second then the first, second and third and so on.