Hello PT,
Thank you for your help with this. I tried align_epi_anat.py with ginormous move, anat_has_skull no, and epi_strip None and still didn't have luck with good alignment (see image).
align_epi_anat.py -epi2anat \
-epi pb02.sub002.r01.despike+orig \
-anat sub002t1_ns+orig \
-epi_strip None \
-anat_has_skull no \
-epi_base 0 -volreg off -tshift off \
-ginormous_move \
-cost lpc -multi_cost lpa lpc+ZZ mi
The raw scans have better alignment than the processed ones (but still not good).
I'm going to try your other suggestion of SSwarper next and see how that goes. Will keep you posted.
Best,
Jessi
