Added automatic registration option & logic.
Added further automatic registration logic, with RegistrationParameters class.
Changed default imput parameters.
Changes for default reading directories.
Added logic for automatic registration of all phases.

Added logic for dirqa on all phases. There are some bugs to be sorted.
Debuging on automatic registration.
Added Color for display node id
Large Commit. Changed everything, so it can do "one click registration". It looks through folder for appropriate files (ct, warped images & vector fields) for subject hierarchy.
Everything is set for Pig experiment.
Large commit. Added logic for automatic registration and dirqa.

Automatic registration is done with seperate class (located at the end of the script).

Dirqa is done either on 01 phase (when there are only two) or on phase "05" when there are more.
added check for directories.
Debbuging.