BUG:  Not region clipping missed brain mask inversion step

The "NOT" probability regions needed to have the eroded
brain mask inverted, otherwise all the "NOT" regions were ending up to be zero.
ENH: Use maximum allocatable cpu for processing.
BUG:  Key image was not being choosen correctly for BRAINSABC.
BUG: intra-subject registrations were incorrect

Intra-subject registrations were being done incorrectly because the
transformes were accumulated with a push operations on the list, and then
the final good transformations were also pushed onto the end of the list
rather than replacing the initial values.
BUG: Fix reference atlas bug for codes of resulting regions.
ENH: Update Reference atlas.