Femur ROI registratio: Implemented a dedicated menu item with parameters suitable for this application.  Default parameters provide speed of under 5 min on the WALS1-WALS2 sample.
Speed is variable and defined by the precision of the AutoFocus stage (such as rotation precision and range)

ROI->ROI registration:  during the reslicing operation in AutoFocus\Finetune iteration ROIs are transformed and partial volume voxels appear while the majority of voxels still remain binary ROI. Calculating of signal difference in the obvious way was not fast enough for comparing the massive images for Femur registration problem.
Developed the Signal difference calculation working directly with Run-length representation of ROIs (x10-20 memory compact) that resulted in x10 speed up during the AutoFocus on Subscale=3. Speed up is even higher on the Finetune phase approaching x30.