Hi, Peter and Taylor
I tried the method on different sessions but I found this method is not quite robust. The alignment is strongly influenced by the initial starting point and alignment can easily fall into local minima. Can you elaborate more on how to manually nudge and set a good starting point for either aling_epi_anat or 3dAllineate??
I am working on some 7T data. Acquiring only a few slices is very common in ultra-high field MRI. It might be quite useful to develop some utilities to align partial coverage data.
ruyuan