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: testing to use numpy tester directly without extensive customization
fix: cleaned up nipype testing framework
fix: clean up fsl model tests.
fix: changed input name for 3dallineate
tst: added missing doctest file maps.nii
Merge pull request #564 from satra/fix/testing

FIX: updated testing so that nipype.test(doctests=True) works fine
tst: added doctest ellipses to fix afni tests
Merge pull request #566 from satra/fix/testing

tst: added doctest ellipses to fix afni tests
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.