Align 2 fMRI runs?


I have two fMRI runs that I’m analyzing using afni proc. I’ve noticed in some instances the EPI’s of the two runs are not aligned with eachother. Also, I have been using Align Anat2Epi, which means the two EPI’s remain in non-warped form.

What’s odd to me, is that after looking the stats, the results don’t look all that bad (i.e. the activation is where I would expect it to be despite one of the EPI’s being completely unaligned to the other EPI).

Since I have two fMRI runs, is it more appropriate to align them both to Anat so they are aligned properly when being analyzed, or is AFNI_proc already aligning the two EPI’s together? I can’ find any commands that would suggest the latter…

Also, is there a way to use and align epi2anat without a volreg input? I’ve been using Slice motion correction (SLOMOCO) for my motion correction and I was advised not to run 3dvolreg on the data after I run SLOMOCO. Should I just use with -epi2ant and then run the output through with the align and volreg blocks?

Thanks for your help