wip: command line version almost there!

connectome_meta.bash --tract-meta-stages 12 -k --m1 DWI --m1-lower-threshold 0 --m1-upper-threshold 1 --angle-threshold 35 -v 10 -O /chb/users/chris/dev/users/nicolas/connectome/_log-1787/ -L /chb/users/chris/dev/users/nicolas/connectome/_log-1787/ -R _log -F -notalairach -o _log -D /chb/users/chris/dev/users/nicolas/connectome/_log-1787/input -d 593000-000024-000010.dcm -1 312000-000008-000044.dcm -f

some issues in the args ordering...
reorder args