Hi Rick,
Please disregard my most recent reply! Now we figured out what the problem is here. In our design, the 3.0 in our 3dmerge command should correspond to NN 2 on AFNI, instead of 3. And that is why there was a mismatch when I did NN 3. There was never a problem before because in what I have done, probably because there were no clusters of voxels that touched at corners and thus NN 2 and NN 3 did not make a difference.
Thank you so much for your help!
Have a great rest of the day!
Best,
Marina