afni.nimh.nih.gov

I think the issue for 3dvolreg is that the volumes have different obliquities. The volumes probably get registered well, but the output might not have the correct obliquity anymore.

For kicks, try this:

3dcalc -a ../localizer_results/ref.results/vr_base_min_outlier+orig -b 1.volreg_twopass \
-expr b -prefix 2.vr.twopass.grid

So 2.vr would have the data from 1.volreg, but should have the grid from the localizer.
Does that overlap well with the localizer?

- rick