Hi! My functional data are in RPI orientation (as per 3dinfo -orient) & have been warped to MNI space. I'm trying to make masks in two different ways:

(1) Making anatomically-based ROIs using regions from the TT_Daemon, which has more of the regions I need, then warping them to MNI space using 3dWarp -tta2mni
(2) Making spherical ROIs using MNI coordinates from relevant literature

I've read that AFNI defaults to RAI. Moreover, in using "Jump to (MNI)," I think I'm noticing small differences in where the coordinates are ending up on the brain relative to where to expect them.

Given all this, is there something I should be paying attention to or changing to make sure that everything I'm doing is legit? For example, should I reorient all my functional datasets to RAI? Or the warped masks to RPI? Or should I adjust the coordinates from the literature -- in what way? -- so that they're consistent w/ RPI?

Thanks in advance! -Robie