add mri_surf2vol wrap
added identity input to Surface2VolTransform
3DROIstats fix
fixed tests
added missing test
wrong path
fixed list outputs
Fixed template for -o argument of fsl_glm
Removed the extension
Merge https://github.com/stymy/nipype

Conflicts:
	nipype/interfaces/afni/preprocess.py
fixed pull request issues:
wrapping Surface2VolTransform,
-moved from preprocess.py to utils.py
-improved input descriptions
-renamed output suffix
fixed errors from DOCTEST, now OK.
add: pycharm .idea/ directory to .gitignore
fix: typo in fugue parameter
fix: warp/unwarp arg parsing for use w/o an in_file
tst: auto test generation for FUGUE
fixed output truncation
Fixing path issues for CMTK Parcellate dilated ROI files
Removed ipdb trace
Added GenerateDirections, FindShPeaks, Directions2Amplitude interfaces
wrapping gendir, find_SH_peaks and dir2amp mrtrix commands.

Also fixed issues with out_filename argument for all interfaces