wip
Added FSL output type NIFTI to dmri mrtrix example
fix: avoid stopping of nipype-workflow caused by temporarily suspended LSF-jobs, And changed logfile of lsf-jobs from <lsf_jobid>.out to <scriptname>.log
fix: spm_realign code to handle 3d files without registering to mean
fix: spm_realign always reslices to the first volume even if register_to_mean rtm is set to True
Merge branch 'master' into spm/reslicetoref

* master: (131 commits)
  fix: added svg neurodebian logo
  fix: notebook links to latest version
  enh: updated tutorial
  fix: broken test to reflect interface changes.
  Slight correction to previous PR
  Fix SPM interfaces
  fix: mark's last name
  fix: updated tutorial to include download of data
  enh: added tutorial notebook
  fix: reverted fix while keeping changed meta tag.
  each time I use an afni interface I have not been using for a long time I spend 4 hours fixing some bugs that goes down to base interface specs......
  fix tcorrmap for use of source_name, depends on recent fix cline_bug branch
  where does source_name come from? should fix a lot of gen_file in afni other than out_file
  fixe name_source traits
  fix the TCorrMap histogram options
  doc: update information on output options for CommandLine interfaces
  tst: added doctest ellipses to fix afni tests
  tst: added missing doctest file maps.nii
  fix: changed input name for 3dallineate
  fix: clean up fsl model tests.
  ...
fixing doc
Function Automask raises error due to string '-apply_prefix <undefined>' generated in the 3dAutomask command
Merge remote-tracking branch 'upstream/master'
Added the option for resampling with isotropic voxels as available in FLIRT but not wrapped in NiPype
Merge branch 'master' into spm/reslicetoref

* master:
  make the test less sensitive to numerical errors
  Fixing typos.
  Cleanup
  simplify using genfromtxt
  Make it more general - calculate moments.
  Added skewness calculation.
  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.
  Make WarpTimeSeriesImageMultiTransform not crash due to wrong return code.
  Added support for non standard return codes. For example when a non zero code is returned but the program has run successfully.
  fix for the which[0]=1 option -> reslice 2..n images
fixing doc
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.
Fixed variable name in PBS plugin.  Now works.
Added note about PBS optional argument for maximum jobname length.
ENH importing basic pieces at a top level
ENH adding external interface namespaces to top-level imports
Put units into descr.
Merge pull request #593 from nih-fmrif/pbs

PBS plugin fixes
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