afni.nimh.nih.gov

I had been worried about whether your datasets covered the
same grid space, but they do.

However, note that 3dOverlap computes the overlap of all
input sub-bricks at once. Since each of your input datasets
has 18 sub-bricks, you are actually computing the overlap
(intersection) of 36 sub-bricks.

If you want to compute the overlap for a specific pair of
sub-bricks, specify that on the command line (for example,
sub-brick 0):

3dOverlap image1.nii'[0]' image2.nii'[0]'

- rick