If you are using only an affine transformation, then you can use Vecwarp to transform lists of coordinates.
https://afni.nimh.nih.gov/afni/community/board/read.php?1,158095,158098#msg-158098
https://afni.nimh.nih.gov/afni/community/board/read.php?1,146048,146181#msg-146181
You can load these tags in from a new file with those new coordinates, or put spheres down instead of "tags" on the new locations.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/rois_corr_vis/suma_spheres.html
If you need to use a transformation that uses both an affine and nonlinear transformations, then you can use the new nl_coords_transform.py. I'll be adding an affine only option, just for convenience there.
