If you have computed an affine transformation to transform between native and standard spaces, you can use one of the methods described in this old post:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,69100,69588#msg-69588
For nonlinear warps, you can use 3dNwarpApply to apply a transformation (getting the right direction, of course). Take a look at this previous post and the class materials ("Back to the original..." slides in afni11_roi.pdf)
https://afni.nimh.nih.gov/afni/community/board/read.php?1,147114,147122#msg-147122
https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni11_roi.pdf