Hi,
On the download page it mentions that Freesurfer v5.3 is not compatible with OS X 10.11 because of an implementation of SIP. As a test, I have run a few subjects with v5.3 under OS X 10.11.3 with SIP enabled but was unable to see any problems, with all test subjects completing without error. I was wondering what I should be looking for (i.e. in the .log etc?) that would indicate that v5.3 is not compatible with OS X 10.11.3.
Thanks.