Hi Ana,

The problem with regressing the WM and ventricles form the previous errts.tproject time series is that motion, polort, and any other previously removed signals that are in the WM and ventricle time series will be re-introduced into the result (unless you regress the original model out of those 2 new time series first).

It would be better to re-run the previous 3dTproject option with the addition of 1 or 2 more -ort options, to include the WM and ventricle time series. That way the complete model is specified at once.


Has the question of afni_restproc.py been resolved for you? That is a different program from afni_proc.py. uber_subject.py runs afni_proc.py. The somewhat dangerously named afni_restproc.py is entirely separate, and we plan to remove it from the distribution.


For this FS mask, it is better to give that to afni_proc.py using -anat_follower, as is done in Example 11. That assumes the mask is aligned with the original anatomy input to afni_proc.py.

To use these things, you should probably get away from uber_subject.py (which is not up-to-date with enhancements to afni_proc.py). Try to work with the afni_proc.py commands, directly.

- rick