In case it helps you or anyone in the future, I just worked on this question myself and this seemed to have worked for me:
I ran @SSwarper to transfer my native space anat into MNI. This outputs a .1D file with the warping info. From there I just ran these two lines:
invert the warp so it is MNI>native:
cat_matvec -ONELINE anatQQ.s${sub}.aff12.1D -I>warp_Matrix.1D
apply the inverted warp to the MNI ROI:
3dAllineate -1Dmatrix_apply warp_Matrix.1D -prefix ATL_tocalc -cost lpa -source_automask -master anatSS.s${sub}.nii -source ATL+tlrc
