spm inverse deformation util
merging
trailing comma fix
Merge branch 'master' into spm_interfaces

* master: (24 commits)
  password and username are mandatory through dependence
  Added config option
  Removed doc warning
  Added MySQL interface.
  fixed docs
  Added similarity calculation interface
  pep8
  Extension is now based on the input file name
  Added missing config
  RF: hash check now ensures that job doesn't get executed if local hash check is set and hash exists
  changelog fix
  imports and pep8 cleanup
  Improved error message.
  Added support for a list of 3d files for TSNR calculation.
  fix: added check for inputs within run
  FIX: local hash check uses proper inputs
  fixed trailing parenthesis
  FIX: Afni outputspec fixes
  fixing implicit_masking option formating
  Forced absolute paths for BEM outputs
  ...
mock changes
merge
Merge branch 'master' into spm_interfaces

* master: (138 commits)
  fix: CompCor PCA extraction was erroneous. fixed to save the correct components.
  fix: disabled check for current version due to portalocker issues
  doc: changed class to ref
  doc: minor spell checkings etc while reading
  fix: job submission should use info['node'] to get node
  fix: afni volreg to use gen_fname
  fix: spm new segment only outputs files as .nii
  fix: simplified format arg since trait catches errors
  fix: remove hash value computation on run unless requested explicitly by local_hash_check
  doc: pep8 fmrirealign
  fix: examples
  fix: FmriRealign4d
  fix: nitime test failure when display is missing
  fix: tests
  fixed doctest error with comma after -i in WIMT
  doctest files
  BF -- changed DARTELNorm2MNInputSpec.fwhm to match SmoothInputSpec.fwhm
  doc: added intro slides
  BUG: Explicitly declare arg to fix position
  ENH: Add opt for converting siemans PAR/REC files
  ...
simplify in_file
Revert "simplify in_file"

This reverts commit f1be287f1313d70221aca09e4f45802dadaf4414.
fixing ApplyInverseDeformationOutputSpec bug
merge
Merge branch 'master' into spm_interfaces

* 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 spm_interfaces

* master: (266 commits)
  fixed paths
  Back to dev
  0.7 release
  Code cleanup.
  doc: updated inputs help to indicate FSL and AFNI inaccuracy when using bounds_by_brainmask
  Fix #493
  Fixes #459
  fixed doctests
  changelog
  fix: ants workflows setup
  BF: Fixed several issues with GroupAndStack interface
  DOC: Various clean up an improvements to docstrings.
  DOC: Added example to LookupMeta docstring
  ENH: Allow meta_keys input to LookupMeta be a mapping.
  minor fixes
  deprecated version should be a string, added AFNITraitedSpec for backward compatibility
  docs
  PEP8
  name_source can be a list, make "infolder" a deprecated name
  Removed unnecessary outputsspecs
  ...
Merge branch 'master' into spm_interfaces

* master:
  added maths.MaxImage examples
  test maths.MaxImage for fslmaths -Tmax option
  add maths.MaxImage for fslmaths -Tmax option
  fix: change type of loops,speedup and between loops so its compatible with changes in the nipy code
  changelog
  DOctest fix
  PEP8
  add doc
  DOC: Update info on Condor and its plugins.
  DOC: Fix documentation glitch
  BF: Use unique filenames for DAGMan workflows
  enh: remove logger dump added in 9d6b1a86921982b84f17b75ebf1a515f1d8710f7
  fix in NewSegment warp field output options
  fix: ensure that commandline calls force terminal output if stdout or stderr is required
  fix: failing flirt test
  fix: doctest for commandline
  doc: added change note
  enh: allow commandline interfaces to control terminal output
  adding trim interface that keeps the original dtype storage
inverse deformation field
fixes
Merge branch 'master' into spm_interfaces

* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR #530
  Removed accidentally added files (#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
doctest
pep8
Merge pull request #540 from bpinsard/spm_interfaces

spm interface to apply inverse deformation