Fix bug when showing/hiding neurons loaded by specifying dir rather than list

* make a fake score list to solve this
fix reading gzipped registration files
Remove code that has been moved to nat.utils package (now on github)
Merge branch 'master' of jgit:AnalysisSuite

# By GJAC
# Via GJAC
* 'master' of jgit:AnalysisSuite:
  Fix bug when showing/hiding neurons loaded by specifying dir rather than list
New NrrdSave function
Fix bug re missing arg for NrrdSave (and help)
pmatch->charmatch
one last fix of pmatch/charmatch

* return numbers not values!
Add AmiraRegFromCMTK() and CMTKRegFromAmira()

* originally from FC project
Add HomogenousAffineFromCMTK() as well
Fix mat2dof --inverse switch in AmiraRegFromCMTK
refactor FlipAndORMasks() to extract FlipImagesWithBridgingReg()

* FlipImagesWithBridgingReg uses CMTK to flip the image with an 
  affine registration. The bridging reg is then applied on top 
  of this.
Added shell quoting to CMTKSimilarity
Merge branch 'master' of jgit:AnalysisSuite

# By Gregory Jefferis
# Via Gregory Jefferis
* 'master' of jgit:AnalysisSuite:
  refactor FlipAndORMasks() to extract FlipImagesWithBridgingReg()
  Fix mat2dof --inverse switch in AmiraRegFromCMTK
  Add HomogenousAffineFromCMTK() as well
  Add AmiraRegFromCMTK() and CMTKRegFromAmira()
  one last fix of pmatch/charmatch
  pmatch->charmatch
  Fix bug re missing arg for NrrdSave (and help)
  New NrrdSave function
  Remove code that has been moved to nat.utils package (now on github)
  fix reading gzipped registration files
Corrected minor mistake in function
More sophisticated colour handling for plot3d.neuronlist

* separate col and colpal arguments to allow specification of the groups
  for colour assignment (col) versus the actual colours (colpal, by function
  or (named) vector of colours)
Merge branch 'master' of jgit:AnalysisSuite

# By GJAC
# Via GJAC
* 'master' of jgit:AnalysisSuite:
  Corrected minor mistake in function
  Added shell quoting to CMTKSimilarity
Fix bug in calculating DotProperties in R>3.0

* this is because I was .Calling the BLAS library directly
* I will probably need to find a different solution if I
  ever want to get this onto CRAN
arithmetic for dotprops objects
Simple utility function with.neuronlist operates in context of dataframe attached to neuronlist