What was the command that you used to run?

This error:
** FATAL ERROR: Can't overwrite existing dataset './(null)_000_PAIRMAP+orig.HEAD'
signifies that a file with the given name already exists-- by default, AFNI commands will (mostly) refuse to overwrite existing files unless you explicitly tell them to, by using the '-overwrite' option-- so you should be able to add that to avoid this, I think.

In this case, I also don't know why your default prefix appears to be (null). Did you give an output name, using '-prefix NAME'?

-> "3dDWUncert for 1000 iterations"
This is probably an unnecessarily large value-- not that anything is wrong with this, but it will likely have taken a while to run and more like 300 should be fine enough.

-> " I am tracking the basolateral amygdala (which I made a value of 1 in the mask) and the ventromedial prefrontal cortex (which I made a value of 2 on the mask). Then I had an exclusion area within the mask (the centromedial amygdala which I made a value of -1). Does this sound that I did this part correctly? "
Sounds fine. Are you using '-logic AND', then?

-pt