I tried installing FSL in my Mac, but had installation error. I have tried installing Quartz software, and it didn't help me either. Kindly help me in this regard.

ERROR occurred during installation!
This command returned an error: /Users/niranjan/fsl/bin/mamba env update -n base -f /private/var/folders/gt/4vm51s9s169c1zsj1bm1qhc40000gn/T/tmp06t7a8hv/fsl-6.0.6.2_macos-64.yml

Hi Niranjan,

There can be multiple factors why the installation failed but your issue headline (Mac Ventura) makes me think that its not necessarily Quartz causing the issue (but it still can) because if it is, the error will appear in the post installation i.e., when you are already running fsl from the terminal.

To rule out some potential causes, you have to check if you have an updated python installed in the system. Actually, fsl python library suggests python version 3.7, 3.8, 3.9, 3.10 based on the documentation (https://pypi.org/project/fslpy/). I believe python.org 

Another important thing to consider is to execute running the fslinstaller as an administrator.

It would also help if you know the content of fsl-6.0.6.2_macos-64.yml

Hope this helps.

Hello,

I am having a similar issue with installing FSL in MacOS 12.6. Miniconda installation fails. Screenshot attached. I have xquartz and Python3 installed.
The command to install fsl is: python3 fslinstaller.py


Any input is appreciated.

Hello Kavita,

Would you be able to post fslinstaller_wci59cn3.log? This might give a clue as to what causes the issue. Thanks.

Hi Kavita,
You can install miniconda first. Feel free to check log file as well.
Many Thanks,
Suren

The log file contents are attached.
Thank you for looking into this.

I tried that, unfortunately it is the same error.

Hi,

I have the same problem. I tried to install fsl on two machines, with the same issue. One machine: Ubuntu 20.04 (focal). Second: Windows 10 with Ubuntu installed from Windows Store.

Error: "This command returned an error: home/$user/fsl/bin/mamba env update -n base -f /tmp/tmp0ceysaja/fsl-6.0.6.3_linux-64.yml"

I tried to run the script with python 2.7, 3.7 and 3.10 and with/without admin rights (sudo). I tried to update the system, also did not work.

If anyone have any idea, I would appreciate it. 

Kind regards,
P

Has anyone any clue about this error?

I encountered the same error on a macbook m1 Ventura 13.4.1, installing the fsl-6.0.7_macos-M1. 

The log is as it follows: "

21:06:27 fslinstaller.py: 933:  [stderr]: # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]:     Traceback (most recent call last):
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$Usern/fsl/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
21:06:27 fslinstaller.py: 933:  [stderr]:         return func(*args, **kwargs)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/conda_env/cli/main.py", line 78, in do_call
21:06:27 fslinstaller.py: 933:  [stderr]:         exit_code = getattr(module, func_name)(args, parser)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/conda/notices/core.py", line 109, in wrapper
21:06:27 fslinstaller.py: 933:  [stderr]:         return func(*args, **kwargs)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/conda_env/cli/main_update.py", line 132, in execute
21:06:27 fslinstaller.py: 933:  [stderr]:         result[installer_type] = installer.install(prefix, specs, args, env)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/mamba/mamba_env.py", line 153, in mamba_install
21:06:27 fslinstaller.py: 933:  [stderr]:         transaction.fetch_extract_packages()
21:06:27 fslinstaller.py: 933:  [stderr]:     RuntimeError: Download error (28) Timeout was reached [https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/osx-arm64/fsl-basisfield-2203.1-hcb8d3e5_4.tar.bz2]
21:06:27 fslinstaller.py: 933:  [stderr]:     SSL connection timeout
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]: `$ /Users/$User/fsl/bin/mamba update -n base -f /private/var/folders/8x/3s_r17r166jgs59n1tl1zvhh0000gn/T/tmp316qp81t/fsl-6.0.7_macos-M1.yml`
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]:   environment variables:
21:06:27 fslinstaller.py: 933:  [stderr]:                  CIO_TEST=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:   CONDA_AUTO_UPDATE_CONDA=false
21:06:27 fslinstaller.py: 933:  [stderr]:                CONDA_ROOT=/Users/$User/fsl
21:06:27 fslinstaller.py: 933:  [stderr]:                     CPATH=/usr/local/include
21:06:27 fslinstaller.py: 933:  [stderr]:            CURL_CA_BUNDLE=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:                  INFOPATH=/opt/homebrew/share/info:
21:06:27 fslinstaller.py: 933:  [stderr]:                LD_PRELOAD=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:              LIBRARY_PATH=/usr/local/lib
21:06:27 fslinstaller.py: 933:  [stderr]:                   MANPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/share/man:/Lib
21:06:27 fslinstaller.py: 933:  [stderr]:                           rary/Developer/CommandLineTools/usr/share/man:/Library/Developer/Comma
21:06:27 fslinstaller.py: 933:  [stderr]:                           ndLineTools/Toolchains/XcodeDefault.xctoolchain/usr/share/man:/opt/hom
21:06:27 fslinstaller.py: 933:  [stderr]:                           ebrew/share/man::
21:06:27 fslinstaller.py: 933:  [stderr]:                      PATH=/Library/Frameworks/Python.framework/Versions/2.7/bin:/opt/homebrew/bi
21:06:27 fslinstaller.py: 933:  [stderr]:                           n:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr
21:06:27 fslinstaller.py: 933:  [stderr]:                           /bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/var/run/com.apple.security.cry
21:06:27 fslinstaller.py: 933:  [stderr]:                           ptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security
21:06:27 fslinstaller.py: 933:  [stderr]:                           .cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.c
21:06:27 fslinstaller.py: 933:  [stderr]:                           ryptexd/codex.system/bootstrap/usr/appleinternal/bin
21:06:27 fslinstaller.py: 933:  [stderr]:        REQUESTS_CA_BUNDLE=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:             SSL_CERT_FILE=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]:      active environment : None
21:06:27 fslinstaller.py: 933:  [stderr]:        user config file : /Users/$User/.condarc
21:06:27 fslinstaller.py: 933:  [stderr]:  populated config files : /Users/$User/fsl/.condarc
21:06:27 fslinstaller.py: 933:  [stderr]:           conda version : 23.1.0
21:06:27 fslinstaller.py: 933:  [stderr]:     conda-build version : not installed
21:06:27 fslinstaller.py: 933:  [stderr]:          python version : 3.10.12.final.0
21:06:27 fslinstaller.py: 933:  [stderr]:        virtual packages : __archspec=1=arm64
21:06:27 fslinstaller.py: 933:  [stderr]:                           __osx=13.4.1=0
21:06:27 fslinstaller.py: 933:  [stderr]:                           __unix=0=0
21:06:27 fslinstaller.py: 933:  [stderr]:        base environment : /Users/$User/fsl  (writable)
21:06:27 fslinstaller.py: 933:  [stderr]:       conda av data dir : /Users/$User/fsl/etc/conda
21:06:27 fslinstaller.py: 933:  [stderr]:   conda av metadata url : None
21:06:27 fslinstaller.py: 933:  [stderr]:            channel URLs : https://fsl.fmrib.ox.ac.uk/fsldownloads/...
21:06:27 fslinstaller.py: 933:  [stderr]:                           https://fsl.fmrib.ox.ac.uk/fsldownloads/...
21:06:27 fslinstaller.py: 933:  [stderr]:                           https://conda.anaconda.org/conda-forge/o...
21:06:27 fslinstaller.py: 933:  [stderr]:                           https://conda.anaconda.org/conda-forge/n...
21:06:27 fslinstaller.py: 933:  [stderr]:           package cache : /Users/$User/fsl/pkgs
21:06:27 fslinstaller.py: 933:  [stderr]:        envs directories : /Users/$User/fsl/envs
21:06:27 fslinstaller.py: 933:  [stderr]:                           /Users/$User/.conda/envs
21:06:27 fslinstaller.py: 933:  [stderr]:                platform : osx-arm64
21:06:27 fslinstaller.py: 933:  [stderr]:              user-agent : conda/23.1.0 requests/2.31.0 CPython/3.10.12 Darwin/22.5.0 OSX/13.4.1
21:06:27 fslinstaller.py: 933:  [stderr]:                 UID:GID : 501:20
21:06:27 fslinstaller.py: 933:  [stderr]:              netrc file : None
21:06:27 fslinstaller.py: 933:  [stderr]:            offline mode : False
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]: An unexpected error has occurred. Conda has prepared the above report.
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:28 fslinstaller.py: 167: 
ERROR occurred during installation!
21:06:28 fslinstaller.py: 167:     This command returned an error: /Users/$User/fsl/bin/mamba env update -n base -f /private/var/folders/8x/3s_r17r166jgs59n1tl1zvhh0000gn/T/tmp316qp81t/fsl-6.0.7_macos-M1.yml

21:06:28 fslinstaller.py:2297:   File "/Users/$User/Downloads/fslinstaller.py", line 2289, in handle_error
    yield
  File "/Users/$User/Downloads/fslinstaller.py", line 2387, in main
    install_fsl(ctx)
  File "/Users/$User/Downloads/fslinstaller.py", line 1786, in install_fsl
    ctx.run(Process.monitor_progress, cmd,
  File "/Users/$User/Downloads/fslinstaller.py", line 1377, in run
    return process_func(admin=self.need_admin,
  File "/Users/$User/Downloads/fslinstaller.py", line 905, in monitor_progress
    raise RuntimeError('This command returned '

21:06:28 fslinstaller.py: 167: Removing failed installation directory /Users/$User/fsl
21:06:28 fslinstaller.py: 764: Running rm -r /Users/$User/fsl [as admin: False]

".

I tried using Python3 (different versions) and Python2.7.

Thank you for any suggestion.

Originally posted by Niranjan Savarirajalu:

I tried installing FSL in my Mac, but had installation error. I have tried installing Quartz software, and it didn't help me either. Kindly help me in this regard. ERROR occurred during installation! This command returned an error: /Users/niranjan/fsl/bin/mamba env update -n base -f /private/var/folders/gt/4vm51s9s169c1zsj1bm1qhc40000gn/T/tmp06t7a8hv/fsl-6.0.6.2_macos-64.yml

Was this ever solved? I'm getting the same error now on Sonoma 14.1.1

Try updating your system and reinstalling FSL and also check Quartz software is correctly installed and check for any specific installation instructions provided by FSL for Mac Ventura 13.1 check FslInstallation/MacOsX - FslWiki (ox.ac.uk)