WIP: Add dwi workflows

[josephmje]

To do:

• remove unnessary changes
• add CLI options previously in click to argparse
• migrate fieldmap workflows to sdcflows
• remove experimental synb0 steps

[oesteban]

Hi @josephmje, great job at solving conflicts. Now that this is in a sane state, could we maybe split this humongous PR into more digestible pieces? Otherwise, I can't commit to review this anytime soon.

[arokem]

+1 Maybe we could start by getting all the infrastructure stuff (docs, CI, etc.) merged in first? And then, once that's in, start dealing with meat of it, bit by bit?

[oesteban]

+1 to the start with the infrastructure first - basically travis tests.

I would hold documentation off just a little while because in nipreps/smriprep#65 we are testing the maintenance of documentation without readthedocs.

That would allow going to the meat a bit faster :D

[josephmje]

+1 I've been finding more and more bugs with this PR so that's definitely for the better. Closing this.

[oesteban]

Hey @josephmje this (as in "further PRs") is awaiting nipy/nipype#3034 and nipy/nipype#3031, isn't it?

[josephmje]

@oesteban yes it is. But for now, I've got an fsl.py and mrtrix.py script that contains the interfaces I was using.