wip
fix for the which[0]=1 option -> reslice 2..n images
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
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
doc: update information on output options for CommandLine interfaces
fix the TCorrMap histogram options
fixe name_source traits
Merge branch 'cline_bug' into afni/tcorrmap

* cline_bug:
  fixe name_source traits
where does source_name come from? should fix a lot of gen_file in afni other than out_file
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......
Merge pull request #568 from bpinsard/cline_bug

Cline bug name_source
fix: reverted fix while keeping changed meta tag.

@bpinsard - reverting the fix while keeping name source. too many doctests started failing. the intent of spec.genfile or spec.name_source is when the input is undefined, not when its defined.
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.