I have tried to run this command 2 times and it does not seem to finish the command.  The log file just says:
Em registration (date/time)
CA Normalization (date/time)
CA Reg (date/time)

The log file ends each time with
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4319 voxels, overlap=0.599)
aligning Right_Thalamus_Proper...
source mean =83.5658, std = 26.5322
X:99-132; Y:128-155; Z:103-141
gca peak = 0.06253 (102\n\n

then that is it.  No formal error presents but there is nonprogression.  Any ideas?  Thanks (again...and again)