In the command you gave

3dmaskave -mask threshold+orig -q raw+orig > mean_oner_ALL_voxels.1D

only the voxel which have a nonzero value in threshold+orig will be averaged from the input raw+orig. When you created threshold+orig, did you actually threshold it -- that is, set some voxels to zero based on their value? If not, then what you want is to use the -mrange a b option to 3dmaskave, so as to say "only keep those voxels whose values are between a and b"; for example, if threshold+orig is a t-statistic, you might want

3dmaskave -mask threshold+orig -mrange 4 99 -q raw+orig > mean_over_SOME_voxels.1D

If you want more complex thresholding (e.g., keep all voxels with values between -99..-4 AND 4..99), then you'd have to use 3dcalc to do the thresholding first. For the advanced AFNI user, this could be done on the command line, as in

3dmaskave -mask '3dcalc( -a threshold+orig -expr astep(a,4) )' -q raw+orig > mean_over_SOME_voxels.1D

When you understand this, you will have passed your first test, on the way to the exalted rank of AFNI Certified Expert (ACE), grasshopper.