fixing ApplyInverseDeformationOutputSpec bug
adding forward warping option to fugue
add fieldmap and shiftmap outputs to Fugue
Merge branch 'master' into fsl_b0

* master:
  fixing spm.utils *OutputSpec inheritance
allow FUGUE to run without in_file
allow FUGUE to run without in_file
allow FUGUE to run without in_file
allow FUGUE to run without in_file
added fsl sigloss to utils
Merge branch 'master' into fsl_b0

* master:
  doc: updated release to dev
  rf: updated version info across programs
  doc: updated changelist to highlight important changes since last release
  Autogenerate setup.py for slicer
  fix: all of stdout captured in subprocess call closes #181
  fix: diffusion imports in slicer
  ENH: Respect user supplied -o -e flags in qsub_args
added SigLoss to __init__
bugfix abspath
Merge branch 'master' into fsl_b0

* master:
  bug in output filename format
  fixing maths command out_file abspath
  fixed abspath for setting outputs
  Fixed AFNI extension
  Added support for BRIK/HEAD to copyfile
  Changed AFNI default output type to BRIK/HEAD
  added missing "exists" parameters, removed extra "other" inputs
  Cleanup and return abspath.
fixing abspath bug
merge
Merge branch 'master' into fsl_b0

* master: (22 commits)
  fix: label2vol test
  fix: randomise - removed os.getcwd
  fix: label2vol mistake
  fix: randomise outputs
  sty: white space
  BUG: Process Directories as data sinks
  fixed matlab example
  DOC: fix link to caching example
  fix: afni tests
  fix: use correct outfile name generation routine
  fix: first filename bug
  fix: absolute path on outputs from fslmaths
  fix: changed sge to use subprocess directly
  fix: check for pbs
  fix: example fixed to import TraitedSpec
  fix: refined pbs to directly use subprocess instead of CommandLine
  Fixed mapnode isdefined bug
  fix: added check to trap exception when mapnode cannot retrieve inputs
  option to change NaNs to zeros in Maths interfaces
  option to change NaNs to zeros in Maths interfaces
  ...
Merge branch 'master' into fsl_model

* master: (209 commits)
  fix: label2vol test
  fix: randomise - removed os.getcwd
  fix: label2vol mistake
  fix: randomise outputs
  sty: white space
  BUG: Process Directories as data sinks
  fixed matlab example
  DOC: fix link to caching example
  fix: afni tests
  fix: use correct outfile name generation routine
  fix: first filename bug
  fix: absolute path on outputs from fslmaths
  fix: changed sge to use subprocess directly
  fix: check for pbs
  fix: example fixed to import TraitedSpec
  fix: removed extra parenthesis
  fix: refined pbs to directly use subprocess instead of CommandLine
  Fixed mapnode isdefined bug
  Added hash_files description.
  Fixed output files hashing and returned paths.
  ...
merge
Merge branch 'master' into fsl_b0

* master: (53 commits)
  Added a test for SPM bool conversion.
  Call super for all SPM _format_args()
  call super
  Make all Booleans to be formated as 1,0 in SPM
  updated changelog
  fix: added test for deepcopy bug
  fix: added back deepcopy
  fix: thanks to @rkern we now have a passing test with dynamic traits retaining their type through pickling
  fix: test that fails when traitedspec is not pickled properly
  updated changelog
  Added a default to maintain backwards compatibility
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  added mention about the new interface to the changelog
  Added tests stub files
  Make check-before-commit
  Significantly faster smoothing in tessellation_tutorial with MeshFix, CFF output option
  Interface for MeshFix by Marco Attene, Mirko Windhoff, Axel Thielscher
  Fixed deprecated config option.
  ...
Merge branch 'master' into fsl_model

* master: (53 commits)
  Added a test for SPM bool conversion.
  Call super for all SPM _format_args()
  call super
  Make all Booleans to be formated as 1,0 in SPM
  updated changelog
  fix: added test for deepcopy bug
  fix: added back deepcopy
  fix: thanks to @rkern we now have a passing test with dynamic traits retaining their type through pickling
  fix: test that fails when traitedspec is not pickled properly
  updated changelog
  Added a default to maintain backwards compatibility
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  utils.Merge option for not flattening the output list
  added mention about the new interface to the changelog
  Added tests stub files
  Make check-before-commit
  Significantly faster smoothing in tessellation_tutorial with MeshFix, CFF output option
  Interface for MeshFix by Marco Attene, Mirko Windhoff, Axel Thielscher
  Fixed deprecated config option.
  ...