Hi Josh,
If your AFNI is current, then the problem is on our side. There was a problem with the build on linux machines that I did not notice until now. This will be fixed by the morning, but in the meanwhile, if you used @update.afni.binaries -d to update your code, you will find a copy of your previous 3dSkullStrip under abin/auto_backup (with abin/ being the directory where your AFNI binaries reside). Move 3dSkullStrip back into abin/ and you should be OK.
cheers
Ziad
Edited 1 time(s). Last edit at 12/17/2013 03:06PM by rick reynolds.