Q: One of the patients used his left leg to perform the task, whereas
   the controls all used their right legs.  We would like to analyse
   the data as if the patient had also used his right limb. What do we
   do?

A: There is a minc tool that will allow you to "flip" the image so that
   what was on the left side will appear on the right side.  It is
   called flip_volume and you use it like this:

Usage: flip_volume input.mnc output.mnc
 
     Interchanges voxel values with their left-right opposites,
     thereby flipping the volume.