FSL doesn't support zsh by default, so I patched it for installation.

FSL installer patch to support zsh

@@ -1066,6 +1066,7 @@ class FslInstall(object):
     shells['ksh'] = '.profile'
     shells['csh'] = '.cshrc'
     shells['tcsh'] = '.cshrc'
+    shells['zsh'] = '.zshrc'
     
     shellmap = {}
     shellmap['bash'] = 'sh'
@@ -1073,6 +1074,7 @@ class FslInstall(object):
     shellmap['tcsh'] = 'csh'
     shellmap['sh'] = 'sh'
     shellmap['csh'] = 'csh'
+    shellmap['zsh'] = 'zsh'

Didn't work for me:

➜  ~ python Downloads/fslinstaller.py
--- FSL Installer - Version 2.0.21 ---
[Warning] Some operations of the installer require administative rights, for example installing into the default folder of /usr/local. If your account is an 'Administrator' (you have 'sudo' rights) then you will be prompted for your administrator password when necessary.
[OK] Installer is current
Where would you like to install FSL? [/usr/local]: /Users/fernando/FSL
Downloading FSL version 5.0.9 (this may take some time)
Checking download...        
[OK] Download is good.
Installing FSL software...
[OK] FSL software installed.
Creating Application links...
Password:
Checking for X11 windowing system (required for FSL GUIs).
[OK] X11 software (required for FSL GUIs) is installed.
Setting up FSL software...
[FAILED] Failed to update your profile zsh with FSL settings
➜  ~ 

Same error: Failed to update your profile zsh with FSL settings
Mac version: macOS Sierra 10.12.3

This worked for me. Modify fslinstaller.py as follows and then run it:

1. In def shell_config(), add zsh to the conditions
2. In def get_profile(), add these lines after declaring the homevariable:

if shell == 'zsh':
    profile = os.path.join(home, '.zshrc')
    return profile

Let me know if that worked for you!

Thanks fepegar, this easy fix worked well!