fix for the which[0]=1 option -> reslice 2..n images
3drefit does not accept -prefix option, since it operates on its own file
now it will work if you give the same out_file name as in_file name
however if you give no out filename it might not work if your
infile is a .nii or .nii.gz since afni will make briks
fix the TCorrMap histogram options
Merge branch 'cline_bug' into afni/tcorrmap

* cline_bug:
  fixe name_source traits
Merge branch 'cline_bug' into afni/tcorrmap

* cline_bug:
  where does source_name come from? should fix a lot of gen_file in afni other than out_file
fix tcorrmap for use of source_name, depends on recent fix cline_bug branch
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: outputs never sets outfile if defined.
rf: refactored automatic file name generation in base class
Merge pull request #563 from alexschaefer83/master

interfaces.afni 3drefit was not running
Merge pull request #569 from bpinsard/afni/tcorrmap

Afni/tcorrmap
enh: updated tutorial
Merge pull request #581 from satra/enh/tutorial_notebook

enh: updated tutorial
fix: notebook links to latest version
fix: added svg neurodebian logo
Merge pull request #582 from satra/enh/tutorial_notebook

fix: added svg neurodebian logo
Merge branch 'master' into bug/spm/realign

* 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.
  ...
fix output listing
Merge pull request #583 from bpinsard/bug/spm/realign

Bug/spm/realign
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.