added more options to kmesh

added options are
    -indexToPoint
    -pointToIndex
    -translatePoints
    -importPoints
    -exportPoints
major refactoring to run cortical thickness tool

1) set the number of threads to 1 for measureThicknessFilter, which
causes a SIGSEGV error in multi-threaded execution.
2) removed unnecessary dependency to vtkPointAttribute.py using kmesh
3) Automatic surface smoothing is performed
4) More additional improvements in logging and execution