Thanks for the helpful links. I did double check through everything and it all looks correct; Sorry about the log file I needed to change permissions on it. Here is the log file from the first email and here is an additional one from today as well as some screenshots:

After running it once and getting the “terminated by signal 9” error when I try to run it again packages have disappeared out of the freesurfer/bin causing more issues. 

The command they are running is make recon-all -k. If you need to see the makefile or other things let me know and I will get them for you.