Hi Yuan,

Yes, it is difficult to match the ventricles very well especially when the target and subject images are very different in ventricle size.  The number of iterations at each level can be controlled using options: -iter8 -iter4 -iter2 -iter1

For example by specifying: -iter1 2, the program will run the last (highest resolution) iteration twice.  

If you specify: -iter2 3 -iter1 0, then the program will skip the last iteration (-iter1 0) but run the iteration at the second highest resolution level 3 times (-iter2 3).   

But I doubt this will make a big difference in the results as far as matching the ventricles better.

Babak