Hi Alex, 

The brain mask does not have to be binary, the algorithm takes non-zero values to perform the masking. However, since you are providing the mask, you need to make sure that it is registered to the ACPC space. This may be the source of error to the EMSPartial_masking being empty. 
As for the adult skull stripping atlas, we currently don't have one, you could still try with the 1yr old but I recommend to use T2 image as well. 

Best,