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
Added support for non standard return codes. For example when a non zero
code is returned but the program has run successfully.
Make WarpTimeSeriesImageMultiTransform not crash due to wrong return
code.
fix: outputs never sets outfile if defined.
rf: refactored automatic file name generation in base class
Support multiple metric arguments per stage.
Segment in SPM interface throws error.
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.
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
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
Merge remote-tracking branch 'upstream/pr/580' into enh/openfmri

* upstream/pr/580:
  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.
Merge pull request #580 from mick-d/master

Correct Class Segment in spm.preprocess
Merge remote-tracking branch 'upstream/master' into enh/openfmri

* upstream/master:
enh: added transformation of individual copes and varcopes to standard space via anatomical image
enh: updated openfmri workflow example to work with current directory and fileformat structure and to register copes and varcopes to mni space