Hi Daniel,

Thanks for your reply.

I think I will also leave the autoweight option alone: I don't have a specific autoweight setting in mind I wanted to use, I was investigating whether it could improve alignment (in light of the warning aea threw up).



Basically, I think my epi-anatomical alignment is ok (I am unsure if it is close enough as I am new to fMRI), but would love any tips on things I can try to improve it.



I have tried changing the cmass, deobliquing options within aea - all to no effect as they are, as we discussed, being taken care of by aea.

I also tried using lpc+ZZ instead of lpc as the cost function, but this produces a catastrophically misaligned epi-anatomical. Not sure what I did wrong there (code below). The anatomical is clipped, so I tried zero padding it before running, but this did not work either.



Any tips to get lpc+ZZ to work, OR other suggestions to try improve alignment would be very appreciated.

Thank you for your patience,

Harriet


------------
code:

afni_proc.py -subj_id $subj \
-blocks align \
-dsets $data_dir/P007_FR_RUN* \
-tcat_remove_first_trs 0 \
-copy_anat $data_dir/FR_uniden_avg \
-anat_has_skull yes \
-align_opts_aea \
-cost lpc+ZZ \
-ginormous_move \
-partial_coverage