* initial start on the LSQ6 module. This should provide function that can be used in MBM 2 (the re-write of MICe-build-model.pl in pydpiper), and should be able to run as a standalone program performing a rigid (6 parameter) registration.  Currently only some initial error checking is performed.
* some small framework updates to the LSQ6.py module
* in setupInitModel, added a check to test the existance of the mask for the file in standard space
* added a comment to the function initializeInputFiles to clarify the type of the first input argument
* added LSQ6.py to the list of scripts in setup.py
Added a comment to the PipelineStage class to clarify what the colour attribute is used for
Added the function getHighestResolution which takes a input MINC file and returns the absolute value of the highest (finest) resolution in the file.
* first functional implementation of RotationalMinctracc through the LSQ6 module
* design change to RotationalMinctracc:
  - setting the parameters is based on the resolution of the input files using factors.
  - only one level of blurring is used
* changes to the LSQ6 module:
  - added a new group to the input file to lsq6, to indicate it is not the 'base' anymore
  - added information about defaults to the lsq6 module options
  - added a flag to override the default factors and degrees that are used for rotational_minctracc
* bug fix in the getHighestResolution function
* made it possible to specify 1 or more inputs to the LSQ6 module (was 1-to-1 before)
* added in initial model handling for the LSQ6 module
* the function initializeInputFiles expects the input "args" to be a list. If a string is provided, a file handler is created for each character in the string. Changed this such that if a string is provided, it is converted into a list.
* updated the description in setupInitModel: the native to standard transformation has to start with name_
* changed the type of file handler in setupInitModel to be PipeFH instead of FHBase, because files might need to be blurred etc.
* changed the file handler typ for the target from and input file handler (using initializeInputFiles) to a registration pipe file handler
* created a minc atom for xfmconcat, and moved the code to create a pipeline stage there
* moved RotationalMinctracc to the minc atoms (from hierarchical_minctracc)
* added the posibility of using a mask for RotationalMinctracc
* added the xfmconcat minc atom
* added some very basic error checking to getBlur. In this function it is possible that a blur file or gradient file is being retrieved that has never been created. In that case, a "non existent key access error" will occur. This catches it and gives a bit of detail as to why the code fails.
* renamed getHighestResolution to getFinestResolution in order to make the return value of this function more intuitive.
Merge branch 'develop-lsq6'
removed debug print statement in xfmconcat function
* added the possibility not to execute the command. This would allow you to create the graph, but not actually run anything. Right now quite a number of files and directories are created that are not necessary, this should probably be fixed in the future
* gave the main set of parameters its own group/name
Merge branch 'master' into mbm-redesign

Resolved merge conflicts in:
	pydpiper_apps/minc_tools/minc_atoms.py
	setup.py

Changes from Matthijs: LSQ6 Module, working rotational minctracc, other misc bug fixes and improvements.