ENH: more graceful handling of low intensity variation timepoints
BUG:  Do not output h5 files unless specified '-a 1'
BUG:  Output composite non-collapsed transform given the proper flags.
ENH: direct initialization for SyN
ENH: Change the direct initialization flag name

Since the direct initialization is added for SyN in addition to the
linear transforms, the "initialize-linear-transforms-per-stage" flag
name is changed to the "initialize-transforms-per-stage".
WIP: write syn composite
WIP: Direct initialization of the SyN stage from initialTx