It DOES print out the clip level -- the 5th line of the sample output below:
% 3dAutomask anat+orig
++ Program 3dAutomask: AFNI version=AFNI_2006_03_21_1314 [32-bit]
++ Authored by: RW Cox
++ Loading dataset anat+orig
++ Forming automask
+ Clip level = 27.514389
+ Number voxels above clip level = 2091065
+ Clustering voxels above clip level ...
++ THD_mask_clust: building cluster ...
+ Largest cluster has 2085107 voxels
+ Eroded 498549 voxels
+ Restored 409817 eroded voxels
++ THD_mask_clust: building cluster ...
+ Largest cluster has 1992751 voxels
+ Filled 53585 voxels in small holes; now have 2046336 voxels
+ Filled 361562 voxels in large holes; now have 2407898 voxels
+ Eroded 111475 voxels
+ Restored 111273 eroded voxels
++ THD_mask_clust: building cluster ...
+ Largest cluster has 2407696 voxels
+ Clustering non-brain voxels ...
++ THD_mask_clust: building cluster ...
+ Largest cluster has 5718521 voxels
+ Mask now has 2407943 voxels
++ 2407943 voxels in the mask [out of 8126464: 29.63%]
++ first 28 x-planes are zero [from A]
++ last 17 x-planes are zero [from P]
++ first 70 y-planes are zero [from S]
++ last 0 y-planes are zero [from I]
++ first 0 z-planes are zero [from L]
++ last 0 z-planes are zero [from R]
++ Output dataset ./automask+orig.BRIK
++ CPU time = 15.840000 sec
