ENH: Clean Segment tubes

. Take unecessary steps out of the while loop
. Stop failing when a tube isn't computed since the program might have to
 run for multiple seeds
. Remove unused arguments (seedScaleMask and seedMask)
. Add empty defaults for seedX and seedPhysicalPoint since one should be
empty if the other isn't
. Remove EXECUTABLE_ONLY
ENH: Use lps coordinates when giving points to SegmentTubes
FIX: Fix reading of tre files in slicer

Fixes issue #298
FIX: Fix segment tubes so the tubes have the image transform information

Fixes issue #298
FIX: Fail when no tube is found

Fixes bug introduced earlier to allow all the seeds to be tried.
FIX: Fix crash when saving an empty node

The constructor must initialize the pointer to prevent it from being
not null when compared later (even though it was never initialized).
Merge pull request #300 from vovythevov/fix-segment-tubes

Misc segment tubes fixes