Hi, I ran into an odd problem which I was able to fix but wanted to let others know about.

This is OS X 10.11.4 with Matlab 2016a and FreeSurfer 5.3.

I got the following error when I ran mkcontrast using batch files that previously worked fine:

/private/var/folders/wt/vj5q34fs20x50sh_6rcrtkn80000gn/T/Cleanup At Startup/sh.h4SI0w: No such file or directory.
ERROR running mkcontrast

Looking into the directories in question, I found that while there was no directory named 'Cleanup At Startup’ inside the T directory, there was such a directory inside ‘vj5q34fs20x50sh_6rcrtkn80000gn’.  I’m guessing some version update changed the location of this directory.  I went into T and performed the following command:

mkdir 'Cleanup At Startup'

after doing so, everything worked again.

Cheers!

Joe