Hello Vince,

My guess is that there are some center of rotation shenanigans here. The dfile and the -rotate options perform rotations about the center of the volume. But the -rotparent performs rotations about the center of the datasets rotated in 3dvolreg.

Why does the -rotparent fail for you while the other do not? I cannot tell for sure. Not at this time of the day at least and not without more sleuthing, preferably with anat+orig and the base in my hands. I do have a guess though:

I did notice a suspicious 3dresample with the -master option on the mask data, prior to applying the rotation. I suspect the origin of mask is no longer matching that of anat so aligning it per the 3dvolreg transform in anat.reg would fail to bring mask.rotparent into alignment with anat.reg

Try aligning mask before the 3dresample operation and see what happens.

cheers,
Godot