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'

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!