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
set default option
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
Fixes for SPM ApplyTransform
Updated test for SPM ApplyTransform
Fixed bug with ants initialization

On one hand, invert_initial_moving_transform was used and needed to
be defined. On the other, as there is a xorg spec with initial_moving_transform_com,
it was still failing.
PEP8 formatting
Merge branch 'master' into bug/FixAntsInitialization
fix: updated prov model
fix: updated prov model to allow QNames
fix: update location attribute
Added new workflow for doing recon all on skullstripped data.
added missing new lines
fixes
Fixed the fieldcoeff issue and also removed the linear transforms that are added to the warps. These are unnecessry