Hi Paxton,

As you have correctly noted, when the -acpc -A options are used in ART, it will compute an initial affine transformation followed by a non-linear transformation.  It then combines the two transformations (the affine and the non-linear) into a single non-linear transformation and stores the results as a displacement field in the warp.nii file.  

Therefore, when the displacement field (warp.nii) is inverted using ivf, the inverse transformation (inverse_warp.nii) will already include the inverted affine transformation.  Thus, this issue is automatically taken care of and it is not necessary to supply 3dwarper with the initial affine transformation.

Hope this help.

Best,
Babak Ardekani