Yes, I think you are right. Things look to have straightened out following a reboot:
no transformation. running registration...
iso loaded
MI:274795808
translocation:0.400689 -5.84046 -6.33343
rotation:-0.122021 0.0228507 0.0406832
scaling:1 1 1
shear:-3.72529e-09 1.86265e-09 2.23517e-08
applying linear registration.
0.499456 0.0203307 -0.0114243 -25.9166
-0.0215742 0.495815 -0.0608435 -8.43396
0.00885475 0.0612702 0.496153 -41.9802
saving test1.trk
Warning: --seed_plan is not used. Please check command line syntax.
Warning: --interpolation is not used. Please check command line syntax.
Warning: --random_seed is not used. Please check command line syntax.
Not sure why the three new warnings are appearing at the end - is the command line documentation on the website out of date?
Many thanks for your help!
Ian