Added functions to create nifti transforms into standard RAS orientations.
Merge branch 'master' of github.com:vistalab/vistasoft

* 'master' of github.com:vistalab/vistasoft:
Merge branch 'master' of github.com:vistalab/vistasoft

* 'master' of github.com:vistalab/vistasoft:
  changed the name of the output for fgResampled
  updated functions so that they will return the resampled fiber group
Merge branch 'master' of github.com:vistalab/vistasoft

* 'master' of github.com:vistalab/vistasoft:
  ENH: Fixed a typoe and cleared unfinished work on tensor-based tracography between 2 ROI. NB this is NOT functinal at the moment.
  Changed shiftPhase.m Removed the reference to old code and added the reference to angle.m
  ENH: Working on some files related to MRTRIX to make the tensor -baed trcking work
  ENH: Removed direct call to mrtrix functions in a specific path location. It will now call the defualt system functions.
  ENH: Changes a path call erro to dwi2tensor
  ENH: Added fuction to check the mrtrix processes that were precomputed.
  ENH: Added tensor-based tractography. Improved functionality by adding a more flexible path definiton to saved out the results.
Merge branch 'master' of github.com:vistalab/vistasoft

* 'master' of github.com:vistalab/vistasoft:
  typo fixed in file header
  Ensure that mrSESSION is in the workspace before modifying it
  This file was moved to the DEPRECATE directory and lost in the migration from svn to github. In fact the file is needed as it is called by routines such as xformROIcoords
  ensure that mrSESSION is in the workspace before modifying it
  Bug fix to ensure that turning off Java Features applies to matlab versions 7.0-7.4 as intended, rather than versions greater than 7, which would also include version 8. Hopefully we can soon elimiante all code pertaining to java features in vistasoft
  fixed the output to work properly for images other that dwi data. This was briefly broken by a past update but now is fixed
  ENH: Fixed bug in mrAnatResampleToNifti.m