Use the command
tkregister2 --mgz --s <mysubjectname> --fstal
to compare your MRI with a Talairach template. You will see something like this:
Click on "TARGET" and "MOVEABLE" (bottom middle of display) to switch between the two MRIs.
Click on "CORONAL", "SAGITTAL" or "HORIZONTAL" to switch between views.
You can use the scaling, translation and rotation functions to improve the match between your MRI and the template. However, very few (if any) images will need editing at this stage.
If you do change something, use "SAVE REG" (top left) to save the result. You will then have to run the previous autorecon1 step again.