The current problem of incorrect distortion correction of T1w images most likely lies in the parameters, either the
hcp_unwarpdir. I have also looked at a few field map images and it seems that a few of them have significantly wrapped phase, which means they need to be unwrapped by including the
hcp_echodiff parameter. I assumed that this parameter equaled
3 ms, which is the default value for Philips B0 map sequences, but I keep getting a different error regarding the units. I will look into this issue right now, because I think that phase unwrapping is necessary in your case if you want to perform field map correction.
As for the
hcp_pre_freesurfer step, I think you can run this without field map correction because the structural images do not seem heavily distorted to me.
Do you know when approximately you will be able to run
hcp_fmri_volume? I can try to resolve the issue that you have just mentioned. I think it would definitely help the quality of the results to correct BOLD images, because I have noticed they are more distorted than T1w.