Merge branch 'master' into bug/afni

* master:
  enh: updated openfmri workflow example to work with current directory and fileformat structure and to register copes and varcopes to mni space
  enh: added transformation of individual copes and varcopes to standard space via anatomical image
  fix output listing
  Add deprecation for old output variable modulated_input_image in Segment (to be replaced with bias_corrected_image) and removed exists=True for outputs that are predicated on input settings
  In Segment, include bias-corrected output only if corresponding save_bias_corrected boolean is True. This prevents to throw an error when save_bias_corrected is set to False but Segment still looks for a created bias-corrected output.
  Segment in SPM interface throws error.
  rf: refactored automatic file name generation in base class
  fix: outputs never sets outfile if defined.
  fix for the which[0]=1 option -> reslice 2..n images
fixed some problems when you did not dilate, a file ROIv was expected which was not created. Further the format of the file was transformed to PEP8
added check for dilation==TRUE to ROIv outputs
Merge pull request #598 from alexschaefer83/master

Fix for Dilation
doc: fixed building with Sphinx 1.2
Merge pull request #603 from satra/fix/docbuild

doc: fixed building with Sphinx 1.2
Merge branch 'master' into bug/afni

* master: (27 commits)
  Fixed tests and docs
  remove deprecated stuff
  sty: many pep8 fixes
  CHANGES + __init__
  Put units into descr.
  ENH adding external interface namespaces to top-level imports
  ENH importing basic pieces at a top level
  FIX: strip extraneous whitespace in trait desc
  Added note about PBS optional argument for maximum jobname length.
  BF: moment parameter was ignored.
  Fixed variable name in PBS plugin.  Now works.
  Changes to PBS pipeline plugin.  Added a maximum length to the jobname, using a default value of 15 corresponding to the Torque maximum.  Modified the config file to do a local hash check by default.
  fixing doc
  make the test less sensitive to numerical errors
  Fixing typos.
  Cleanup
  simplify using genfromtxt
  Make it more general - calculate moments.
  Added skewness calculation.
  fixing doc
  ...
Merge branch 'master' into bug/afni

* master:
  doc: fixed building with Sphinx 1.2
  added check for dilation==TRUE to ROIv outputs
  fixed some problems when you did not dilate, a file ROIv was expected which was not created. Further the format of the file was transformed to PEP8
fixing bug, separate gen_file from name_source behavior
Merge branch 'bug/afni' into testing

* bug/afni:
  fixing bug, separate gen_file from name_source behavior
  doc: fixed building with Sphinx 1.2
  added check for dilation==TRUE to ROIv outputs
  fixed some problems when you did not dilate, a file ROIv was expected which was not created. Further the format of the file was transformed to PEP8