fsl_glm interface
Merge branch 'master' into fsl_randomise

* master: (79 commits)
  fix: update to use abspath for out_file
  fix: allow file to be copied for workflow operation (don't allow inputs to be modified)
  fix: add imports to init
  fix: missing test file
  DOC: Added matlab_wrap example that allows for more control and access to MAtlabCommand inputs and outputs
  TEST: added tests for spm utils reslice
  TEST: added tests for spm utils apply_transform
  TEST: added spm util coreg tests
  enh: simple spm_reslice interface
  added catch if spm not found
  ENH: interface to use spm_coreg to calc transform
  enh: set up basic interface
  sty: embed emacs and vim setting in file
  Renamed README so Github can parse reStructuredText format
  fix: epidewarp.fsl
  Fix fixed download link ;)
  Fixed download link
  Release 0.5.3
  Doc: added example to epidewwarp.fsl
  FIX: switched epidewarp to fsl interface
  ...
importfix
importfix
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 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.
  ...
Merge branch 'master' into fsl_model

* master: (57 commits)
  Fixed afni test
  Fixed AFNI tests.
  Escape the expr parameter in 3dcalc.
  fixing TSNR integer data bug
  fix: update getmask to dilate while binarizing
  sty: rest formatting
  ENH: Provide access to all relevant BET outputs when "surfaces" option used.
  Skipping dynamic traits tests for now.
  Fixed failing doctest.
  sty: fixed white space and removed traits fix
  Reverted the traits "fix" workaround.
  Removed redundant example, renamed the antsRegistration template.
  Put interpolation argument back in. Renamed the input/outputspec.
  Added changelog information.
  Revert "fix: added test for deepcopy bug"
  reverted traits change2
  reverted traits change
  ENH: Future proof the API for new template building
  Fixed input/outputspec names.
  Refactoring.
  ...
Merge branch 'master' into fsl_model

* master: (21 commits)
  fix: fsl tests
  sty: white space
  fix: automask bug when apply_mask is not specified
  fix: updated test writer with additional metadata
  fix: remove unnecessary print statement
  fix: trim http link for code
  fix: github url generation
  fix: return full hash
  Removed unnecessary usedefault.
  fixed typo in a file name
  fix: github authentication
  Going back to distinguishing affine transformations by names. Improved docs.
  fixed typo in randomize parameters
  Removed unnecessary copyfiles and added output_image option.
  BF: Pass plugin_args to child nodes of MapNode
  ENH: Don't require ordereddict for python < 2.7
  BF: Fix for plugins when using python2.7
  Fixed parenthesis.
  Fix fslreorient2std output collection
  Allow FNIRT to take standard names as reference.
  ...
Merge branch 'master' into fsl_model

* master: (188 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 fsl_model

* 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
doc and __init__
fix for issue 531
address 533
Merge branch 'master' into fsl_model

* 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
  ...
changelog
Merge branch 'fsl_model'
BF: Fix issue where unicode paths were not recognized as files.

Fixes issue where output files with unicode paths were always
being deleted if remove_unnecessary_outputs was set to True.
Merge pull request #547 from moloney/bf-unicode-paths

BF: Fix issue where unicode paths were not recognized as files.
constrain write_which to length 2
Merge pull request #534 from beOn/whichFix

Fix for #533 - use of write_which and closes #531