So this one is kind of a philosophical question that I’ve been wondering about for awhile that doesn’t have to do with any particular software.
As I’ve done multiple preprocessing workflows I’ve noticed in certain situations that using alignment algorithms (e.g. AntsRegistration, 3dAllineate) using a completely unaligned EPI as the moving image and either the subject anatomy in MNI space or an MNI template as the fixed image gives me better alignment than the common practice of first aligning the EPI to the anatomy then using the ant->MNI transform on the new EPI to get the EPI into standard space. In fact I don’t think I’ve ever seen going straight from EPI->standard space mentioned in the hundreds of tutorials and articles I’ve read.
I understand the conceptual logic for the EPI->anat->MNI tactic in that it’s supposed to give you better alignment because the original EPI and anat are supposed to be close together so aligning the EPI->anat first should give you a fairly good alignment which should then persist if you use the anat->MNI transformation matrix on the new EPI but is there any reason to NOT use a straight EPI->MNI alignment if it gives you better results because isn’t that the point of the process?
I’m actually in this exact situation right now but also it’s something I’ve always been curious about so I wanted to ask people who would know much better than me.