This sounds like the line might not be continuing properly from here:
3dMEMA -prefix SubjectiveFamiliarityHit6vs5 \
-jobs 16 \
-max_zeros 0.25 \
-missing_data 0 \
-set 6vs5 \
SS01 SS01/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[3]' \
SS01/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[4]' \
SS02 SS02/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[3]' \
SS02/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[4]' \
SS04 SS04/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[3]' \
SS04/'decon_SubjectiveFamiliarityHit456_twottests_smartblur4_masked_ANTS+tlrc[4]' \
That would explain the 2 dof (since there are now 3 subjects) and the error message that comes from trying to run the directory SS06 as a script. But in your post it looks like the line should continue properly, so that might not be the problem.
Isaac