Hello,
While I have not gone through the entire script so well yet, it jumped out that you originally aligning each run to volume index 0 for that run. The MIN_OUTLIER volume is generally a much better base volume, as it is expected to have very little motion artifact. Consider this set of options (part of Example 13):
-align_opts_aea -cost lpc+ZZ -giant_move \
-volreg_align_to MIN_OUTLIER \
-volreg_post_vr_allin yes \
-volreg_pvra_base_index MIN_OUTLIER \
-volreg_warp_final_interp wsinc5 \
I hope that works a little better, though for noisy data, I could see averaging being better.
But you have index 86 above. What does that index imply?
- rick