Hi-

You would do this creating a transformation between the two datasets (MNI template and subject anatomical), and then applying that transformation to the ROI dset. Between two different subject brains (like the MNI template and a person), you would probably want to use nonlinear alignment, because the structural differences are so great. Programs in AFNI for this would be 3dQwarp or @SSwarper (the latter being a program that combines skullstripping (SS) and nonlinear warping). When applying the transformation to the ROI dset of interest, you also have to be careful to apply correct interpolation for the data of interest--in this case, integer values within the ROI dset--which we would typically call "NN" = nearest neighbor interpolation.

It might be worth checking out some of the AFNI Academy videos about these concepts and relevant programs here:
for alignment/warping/transforming:
[www.youtube.com]
for atlas/template descriptions and info:
[www.youtube.com]

It might be easier to discuss setting up this particular problem, then. Some further details, like, are you running FreeSurfer on your anatomical and some other things might be useful, too.

--pt