add mri_surf2vol wrap
added identity input to Surface2VolTransform
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
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
Updated new mrtrix interfaces to new out_file format
updated CHANGES log
added dummy files for testing new mrtrix interfaces
autogenerated tests
fix: construct sparse matrix using topological sort order
Merge branch 'master' into fix/sparse_matrix

* master:
  Added tests.
  Fixed a copy/paste error.
  make DataGrabber and SelectFiles use human order
  Update indexsidebar.html
  Fixed Frontiers citation
  Update .travis.yml
Merge pull request #738 from swederik/bf/parcellate

BF: Fixing path issues for CMTK Parcellate dilated ROI files
Merge pull request #747 from satra/fix/sparse_matrix

fix: construct sparse matrix using topological sort order