Hi Bruce, 

Here is what I did. For each subject:

a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory

b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. 

c) Then I ran the following command:

recon-all -all -3T -mprage -s processed/Subnum

I get the following error: