afni.nimh.nih.gov

You do not need the -b variable:

for bash: 3dcalc -a betaCoefficients.nii.gz -b -expr 'a/$( cat referneceValue.1D)' >normalized betas.nii.gz
for tcsh or bash: 3dcalc -a betaCoefficients.nii.gz -b -expr 'a/`cat referneceValue.1D`' >normalized betas.nii.gz

This assumes that there is one and only one properly formatted number in referneceValue.1D