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
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.
  ...