Hi Matt,

I'm glad that you are finding ART useful.  I can understand that 3dwarper may change the voxel values slightly due to interpolation, but what you are describing seems to be more in magnitude than what one would expect as interpolation artifact.   I am surprised that you don't see it in 23 of 25 cases.  Are you sure that the significantly altered intensity values are not due to AFNI?

Anyhow, assuming that this IS interpolation artifact (which I don't think it is), you can use the applywarp3d software (also included in ART) which DOES have the -nn option as follows:

applywarp3d -nn -w $basename""_HBS_10blur_PER4_3dAllineate9x2_wrp.nii  
-o $basename""_HBS_10blur_PER4_3dAllineate9x2_searchwindow10_3dwarped  $basename""_HBS_10blur_PER4_3dAllineate9x2.nii

This program basically applies the non-linear transformation output of 3dwarper (stored in $basename""_HBS_10blur_PER4_3dAllineate9x2_wrp.nii) to the subject image $basename""_HBS_10blur_PER4_3dAllineate9x2.nii and stores the result in $basename""_HBS_10blur_PER4_3dAllineate9x2_searchwindow10_3dwarped.nii

Incidentally, have you tried the -A option with 3dwarper.  If you use this option, the program does an initial affine alignment first before the non-linear registration.  With this option, you may not need the initial AFNI alignment.

Try these idea for now and if the problem still persists let me know.

Best,
Babak