We here at the University of Wisconsin, Madison are constrained to run only compiled Matlab on our clusters. We have a number of groups that use freesurfer on I have just completed creating some workflows to do longitudinal, -localGI and a basic processing using autorecon1,2 and three.

These run in our center on execute nodes not requiring a license since they use the compiled version and a runtime.

For the -localGI:

Besides the basics of running a compiled matlab in terms of setting up the environment right, I had to change

mris_compute_lgi

and some input mappings in some of the freesurfer matlab toolbox. My changes had all the args coming into matlab as strings and I had to find the trouble ones(10 or so) and convert them to the proper expected type .

This allows thousands of jobs to be analyzed at once on our cluster.

Anyone willing to take charge of these changes back at Harvard. It would be great to have this variation available to others.