Hello there!

I recently used afni_proc.py to pre-process my rs-fMRI data. When I visualised the volreg output and overlaid it onto the final anatomical image, I noticed that there is a bit of misalignment, namely the EPI image seems to be "pulled up" (see image).

I tried with various align cost functions, the -epi2anat option, skull-stripped and un-stripped images but it always seems to end up in this situation.

Since the two images are almost perfectly aligned in the raw data, I was wondering whether there is a way to somehow omit the align step (even though I'm aware that the transformation matrix from it is required for the registration at volreg)?

Any help would be greatly appreciated!

Greetings from (a rather unnaturally sunny) London!

Misho