PE-Polar SDC: Unify interface

[oesteban]

Currently, two important inputs are passed by argument (bold_meta, and epi_fmaps) and the other three (in_reference, in_reference_brain, in_mask) are passed by Nipype workflow inputs.

All of them should be workflow inputs.

[mattcieslak]

Any thoughts on replacing bold with distorted and undistorted? A number of interfaces have bold_ref as both inputs and outputs. It might make sense to have inputs be distorted_ref and outputs be undistorted_ref. The boilerplate is also specific to bold, which is confusing when it's included in the html for preprocessed dwi data.

[effigies]

@mattcieslak Perhaps open the bold -> (un)distorted issue separately? This got closed, but the closing PR didn't seem to address it.

[oesteban]

Sorry for closing it, I thought it wasn't going to happen.

Yes, please open a new issue - I did not fully removed the term "bold" from the workflow because it'll take deeper changes to replace the enhance&skullstrip workflow with an equivalent with low b images.