Thank you for your answer and the background information.
I'll watch these videos. After taking a closer look at the registration, the anat-->MNI transformation underperforms quite a bit using 3dAllineate. I may switch to 3dQwarp and 3dNwarpApply to see whether this improves things. I would open a new thread though as this topic has been dealt with successfully :)
Bests,
Philipp
