afni.nimh.nih.gov

Hello,

I will preface by apologizing for the silly question....

My general pipeline uses the align_epi_anat.py script, however, I have 2 animals where the original EPI and anatomical images have better alignment than the output from the align_epi_anat script. Is it necessary to perform alignment between those images prior to registering to a template if it doesn't align as well as the originals do?

Thanks in advance,

Sharyn