Sorry for the confusion!

I don't know what is meant by frequency "8". At what Hertz is your frequency?
>> The stimulus in the experiment has a periodicity at every 42 secs (~.023Hz). Like I said earlier, the data includes 112 time points - (4: stimuli + 10: resting) * 8 times and TR = 3s.

So, firstly, you are processing on a surface?
>> Yes Correct.

And you are picking out the volume with index 8? I don't think you are getting phase information out by just selecting a single volume (unless you have left out intermediate steps). For a real component "Real" and an imaginary component "Imag" from the complex number, the phase is given by: arctan(Imag/Real).
>> The input in the 3dcalc (e.g. $output_dir/pb07.${subj}_${hemi}.${hemi}.r{$r}.DFT.niml.dset) is the output from the 3dDFT (3dDFT -prefix pb07.${subj}_${hemi}.${hemi}.r{$r}.DFT.niml.dset pb06.${subj}_${hemi}.${hemi}.r{$r}.detrend.niml.dset). so I believe the input in the 3dcalc already includes complex number. This is why I calculate the phase at the period of 8 (frequency ~0.023Hz). Does this make sense?

Thanks!!
Taek