3DROIstats fix
fixed tests
added missing test
wrong path
fixed list outputs
Fixed template for -o argument of fsl_glm
Removed the extension
fixed output truncation
enh: update with new neurodebian script
enh: add support for vagrant
fix: remove sudo for bash
fix: cleaned up install script
saving stats in a file
updated tests
add matplotlib
Merge remote-tracking branch 'upstream/master' into enh/vagrant

* upstream/master: (22 commits)
  Reformated inputs and added tests
  fix: fixed autotest for applytopup
  Fixed file extension
  Fixed test files import.
  FIX: topup out file and params
  fixed possible values for -datatype parameter of tracks2prob interface. Previous values were in error. correct values obtained from: http://www.brain.org.au/software/mrtrix/general/formats.html#datatypes
  fix: construct sparse matrix using topological sort order
  autogenerated tests
  added dummy files for testing new mrtrix interfaces
  updated CHANGES log
  Updated new mrtrix interfaces to new out_file format
  Added GenerateDirections, FindShPeaks, Directions2Amplitude interfaces wrapping gendir, find_SH_peaks and dir2amp mrtrix commands.
  Removed ipdb trace
  Fixing path issues for CMTK Parcellate dilated ROI files
  tst: auto test generation for FUGUE
  fix: warp/unwarp arg parsing for use w/o an in_file
  fix: typo in fugue parameter
  add: pycharm .idea/ directory to .gitignore
  fixed errors from DOCTEST, now OK.
  fixed pull request issues: wrapping Surface2VolTransform, -moved from preprocess.py to utils.py -improved input descriptions -renamed output suffix
  ...
added "./" in front of all non absolute output paths for AFNI
fixed doctests
Revert "added "./" in front of all non absolute output paths for AFNI"

This reverts commit a2d7aa357274e3a9fda5f2f9f6020ab88173c0b2.
Revert "fixed doctests"

This reverts commit 552fed3a9b61627d62778009a7fc554038b409cb.