Review FSL eddy interface

Just fixed PEP8 errors in the interface and reviewed the solution
for the bugs, that were already solved.

Please, close #769.
bugfix: for unknown reasons WarpUtils produced wrong command lines
bugfix: for unknown reasons WarpUtils produced wrong command lines (ii)
fix:docstring of traits.Directory was not correctly generated
Merge branch 'master' into fix/ElastixDocumentation

Conflicts:
	nipype/interfaces/elastix/base.py
fix:docstrings
Merge pull request #905 from oesteban/fix/ElastixDocumentation

Fix elastix documentation
Merge branch 'master' into bug/fnirtfileutils
Merge pull request #906 from oesteban/bug/fnirtfileutils

Fix: fsl.WarpUtils
Merge branch 'master' into bug/fixEddyWrapper

Conflicts:
	nipype/interfaces/fsl/epi.py
fix typo
Merge pull request #907 from oesteban/bug/fnirtfileutils

fix typo in WarpUtils input traits
ENH: tidy up fsl-epi tools

* TOPUP: regarding #794, #796 I've cleaned up the docstring and implemented
  the three arguments that were still missing. The problem is that TOPUP
  admits one or more values for them, so the implementation of all the
  traits should be updated.

* Eddy: the implementation of @JensNRAD seems to work out, I reviewed
  the docstring. Close #769.

* Added deprecation notices and minor fixes.
pep8
Merge pull request #909 from oesteban/fix/TidyFSL-EPI

Tidy fsl epi interfaces
Merge branch 'master' into enh/NewEPIArtifactCorrections
updating dmri preprocess example
ENH: N4BiasFieldCorrection new arguments

Now, it is possible to save the estimated bias field, by fully supporting
the --output argument specification.
Merge branch 'enh/N4-output-bias' into enh/NewEPIArtifactCorrections
ENH: new artifact correction workflow on fsl

Uses TOPUP and Eddy for correction. Tested on the new dmri_preprocess.py
example with the fsl course data.