fix: update for use in workflow and reflect new nipype conventions
fix: TOPUP naming and flexibility on extension overloading based on name
fix: more topup naming fixes
Merge branch 'master' into fix/eddy

* master:
  fix: moving save from numpy to pickle
  install ordereddict for py26
  fix: moving save from numpy to pickle
  install ordereddict for py26
  fix: update conda in environment
  fix: parenthesis fixes
  dbg: anaconda to miniconda update
  dbg: conda update
  fix: update conda
  ENH: Large SGE jobs were overloading on qstat
Fixed details in antsRegistration interface

The generation of output filenames was incomplete for inverse outputs
in both collapsed and not-collapsed modes.

Additionally, collapsed mode for only-linear registrations was broken
as the warp file was not generated (but checked for existence)
Minor fix ensuring good values in output

invert_flags in collapse mode got unexpected values (not boolean)
for nonlinear transform
fixed treatment of filename when namesource is not a file
fixed mrtrix direction generator out file treatment. Depends on command
filename previous commit
set default option
tst: updated tests
trailing space is probably making travis fail in #798
test also for parameter based source name for output file
fixing command filename tests
Simplify input of a single LUT. Closes #726
fix: updated apply topup
fix: arg generation
fix: topup workflow
tst: dummy files
few minor spell fixes
Update Vagrantfile