The following got FSL up and running on the 10.11 GM:
0. (may not be necessary) remove FSL
1. Install latest version of XQuartz
2. Download fslinstaller.py
3. Open fslinstaller.py in text editor and change line 1090 to
for release in range(10,16):
and comment out line 1092. Save.4. Run python fslinstaller.py
Good luck!