afni.nimh.nih.gov

Hi Josh,

If only 1 run had poor alignment, that means that 3dvolreg
failed to align across runs, which means there was probably
a very large subject movement between runs.

Try adding -twopass to the 3dvolreg command. And while
you are at it, consider extra zeropadding for that step. So
try adding this set of options to your afni_proc.py command:

-volreg_opts_vr -twopass \
-volreg_zpad 4 \

- rick