Problems installing FSL

Software Support
62

Hi @Shivani_Rajeshree, the error message is telling you that it can’t find the fslinstaller.py script - you need to make sure that you are using the correct path. Is your Windows username Shivani? If so, this should work:

python /mnt/c/Users/Shivani/Downloads/fslinstaller.py

63

Dear all,
I have read through this chat with people having similar problems to me. I have a Mac version 14.5 with plenty of space. I try to install FSL with the following command: python3 fslinstaller.py.
I get the following error:

ERROR occurred during installation!
12:18:25 fslinstaller.py: 206:     This command returned an error: /Users/hwj624/fsl/bin/conda env update -p /Users/hwj624/fsl -f /private/var/folders/96/f8j28zrn2n14h5dhff4q6dym0000gn/T/tmpdw3uq4dw/fsl-6.0.7.11_macos-64.yml

12:18:25 fslinstaller.py:2830:   File "/Users/hwj624/Downloads/fslinstaller.py", line 2822, in handle_error
    yield
  File "/Users/hwj624/Downloads/fslinstaller.py", line 2937, in main
    install_fsl(ctx)
  File "/Users/hwj624/Downloads/fslinstaller.py", line 2200, in install_fsl
    ctx.run(Process.monitor_progress, cmd,
  File "/Users/hwj624/Downloads/fslinstaller.py", line 1623, in run
    return process_func(admin=self.need_admin,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hwj624/Downloads/fslinstaller.py", line 1056, in monitor_progress
    raise RuntimeError('This command returned '

12:18:25 fslinstaller.py:2833: Environment variables:
12:18:25 fslinstaller.py:2835: __CFBundleIdentifier=com.apple.Terminal
12:18:25 fslinstaller.py:2835: TMPDIR=/var/folders/96/f8j28zrn2n14h5dhff4q6dym0000gn/T/
12:18:25 fslinstaller.py:2835: XPC_FLAGS=0x0
12:18:25 fslinstaller.py:2835: LaunchInstanceID=F82446E3-E124-4932-9F47-6B870A3A0338
12:18:25 fslinstaller.py:2835: TERM=xterm-256color
12:18:25 fslinstaller.py:2835: SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.lrd0tfK7Ae/Listeners
12:18:25 fslinstaller.py:2835: SECURITYSESSIONID=186ac
12:18:25 fslinstaller.py:2835: XPC_SERVICE_NAME=0
12:18:25 fslinstaller.py:2835: TERM_PROGRAM=Apple_Terminal
12:18:25 fslinstaller.py:2835: TERM_PROGRAM_VERSION=453
12:18:25 fslinstaller.py:2835: TERM_SESSION_ID=B4F1554F-817D-48BC-B5D5-AC0E92A5291C
12:18:25 fslinstaller.py:2835: SHELL=/bin/zsh
12:18:25 fslinstaller.py:2835: HOME=/Users/hwj624
12:18:25 fslinstaller.py:2835: LOGNAME=hwj624
12:18:25 fslinstaller.py:2835: USER=hwj624
12:18:25 fslinstaller.py:2835: PATH=/opt/anaconda3/bin:/opt/anaconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin
12:18:25 fslinstaller.py:2835: SHLVL=1
12:18:25 fslinstaller.py:2835: PWD=/Users/hwj624/Downloads
12:18:25 fslinstaller.py:2835: OLDPWD=/Users/hwj624
12:18:25 fslinstaller.py:2835: CONDA_EXE=/opt/anaconda3/bin/conda
12:18:25 fslinstaller.py:2835: _CE_M=
12:18:25 fslinstaller.py:2835: _CE_CONDA=
12:18:25 fslinstaller.py:2835: CONDA_PYTHON_EXE=/opt/anaconda3/bin/python
12:18:25 fslinstaller.py:2835: CONDA_SHLVL=1
12:18:25 fslinstaller.py:2835: CONDA_PREFIX=/opt/anaconda3
12:18:25 fslinstaller.py:2835: CONDA_DEFAULT_ENV=base
12:18:25 fslinstaller.py:2835: CONDA_PROMPT_MODIFIER=(base) 
12:18:25 fslinstaller.py:2835: GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
12:18:25 fslinstaller.py:2835: GSETTINGS_SCHEMA_DIR=/opt/anaconda3/share/glib-2.0/schemas
12:18:25 fslinstaller.py:2835: XML_CATALOG_FILES=file:///opt/anaconda3/etc/xml/catalog file:///etc/xml/catalog
12:18:25 fslinstaller.py:2835: LC_CTYPE=UTF-8
12:18:25 fslinstaller.py:2835: _=/opt/anaconda3/bin/python
12:18:25 fslinstaller.py:2835: __CF_USER_TEXT_ENCODING=0x1F5:0x0:0x0
12:18:25 fslinstaller.py: 206: Removing failed installation directory /Users/hwj624/fsl
12:18:25 fslinstaller.py: 897: Running rm -r /Users/hwj624/fsl [as admin: False]
12:18:28 fslinstaller.py: 206: Restoring contents of /Users/hwj624/fsl
12:18:28 fslinstaller.py: 897: Running mv /private/var/folders/96/f8j28zrn2n14h5dhff4q6dym0000gn/T/tmpdw3uq4dw/old_destdir0 /Users/hwj624/fsl [as admin: False]

Can anyone help me solve this problem?

64

Hi @christensen, can you share the full log file from the failed installation?

65

As a new user I apparently cannot upload files. Can I send it to you in another way?

66

Do you have access to a file sharing service, e.g. dropbox, google drive, etc?

67

Hi,

Another person here with a very similar error occurring during FSL installation.

ERROR occurred during installation!
This command returned an error: /home/administrator/fsl/bin/conda env update -p /home/administrator/fsl -f /tmp/tmpdpd0gpkp/fsl-6.0.7.11_linux-64.yml

I am also a new user so cannot attach files, but I included a screenshot with the error and the log file in this Google Drive folder.

https://drive.google.com/drive/folders/1WElkT-hz7RPOcF7uMNyhqpDtSE98T1QX?usp=sharing

Note that I did try the fix you gave David_F above (CONDA_AUTO_UPDATE_CONDA=false ./fslinstaller.py), but that did not work for me. I did install conda relatively recently (a couple weeks ago), so it is possible that the version I have includes the change that broke FSL installation.

Any advice you have would be greatly appreciated.

Anne

68

Does this link work for you? :slight_smile:

69

Hi @anne.a, it looks like your network connection was interrupted during the installation.

The latest version of the fslinstaller script will attempt to resume the installation when this occurs, and also has a new --throttle_downloads option which tries to make the download more robust. Could you download the latest version from here, and run it with the --throttle_downloads option, e.g.:

python fslinstaller.py --throttle_downloads
70

Hi @christensen, I’m not entirely sure why your installation is failing. Are you using macOS Big Sur? It kind of looks like conda is having trouble because of your relatively old OS version.

Could you try re-running the installer like this to see if it solves the problem?

export CONDA_OVERRIDE_OSX=11.0
python fslinstaller.py
71

@christensen Sorry, I just realised that my previous suggestion won’t work. Could you try this instead:

export SYSTEM_VERSION_COMPAT=0
python fslinstaller.py
72

I tried this, but after 4 hours and nothing happened I cancelled the operation. Do you have any other suggestions? I have macOS Sonoma.

73

Can you share the output that was printed, and ideally a copy of the log file?

74

Hi @paulmccarthy, I suspected that was the problem, but my lack of experience makes log files difficult to interpret.

I followed your instructions and it worked like a charm, thank you!

1 Like
75

Dear @paulmccarthy

I ran python ~/Downloads/fslinstaller.py from the command line on a Macbookpro M3 with Sonoma 14.4 and got stuck at step 3 (Installing FSL into /Users/xxxx/fsl). I have installed fsl on multiple machines earlier but never ran into something like this before.

I tried almost all of the solutions posted here but they did not work. Here is my log file.
Could you please kindly suggest?
Highly appreciated!

Chaipat
fsl_installation_20240614011923.txt (19.2 KB)

76

Hi @cchunharas, this looks like an issue with your network connection - one of the downloads seems to have been interrupted. Could you try running the installer like this, to try and make the downloads more resilient? You should not need to use the --miniconda option:

python fslinstaller.py --throttle_downloads
1 Like
79

Problem has been solved. Thank you again @paulmccarthy

80

Hello @paulmccarthy,

I’m also having the similar issues with installing FSL recently. It would be very helpful if you could help me troubleshoot with the errors.

I’m trying to install FSL on a linux cluster, and the OS is Rocky 8.9. Here are the commands I tried:

  1. Used the python3 from /usr/bin/python

    a. Command used: python fslinstaller.py -V 6.0.6 -n
    Error log

  2. Built an empty environment called “fsl_base”, with mamba, and python 3.11. So the python was from /packages/envs/fsl_base/bin/python.

    a. Command used: python fslinstaller.py -V 6.0.6 -n
    Error log

    b. Command used: CONDA_AUTO_UPDATE_CONDA=false python ./fslinstaller.py -V 6.0.6 -n
    Error log

    c. Command used: python fslinstaller.py --throttle_downloads
    Error log

Thanks in advance!
Nil

81

Hi @Nil, if you are trying to install FSL 6.0.6, can you try running the fslinstaller.py script specifying an alternative Python 3.10-based miniconda installer, e.g.:

python fslinstaller.py -V 6.0.6 -d /packages/apps/fsl/6.0.6 --miniconda https://repo.anaconda.com/miniconda/Miniconda3-py310_24.4.0-0-Linux-x86_64.sh

We are updating the release system so that an appropriate miniconda will be automatically selected (and will probably eventually switch to micromamba), so this shouldn’t be necessary in the future.

82

Hi Paul @paulmccarthy,

Thanks for your quick response!

When running the command you suggested in a mamba (1.5.1) made environment with python=3.10.14, I got a similar conda update error:
08:11:30 fslinstaller.py:3209: This command returned an error: /packages/apps/fsl/6.0.6/bin/conda env update -p /packages/apps/fsl/6.0.6 -f fsl-6.0.6_linux-64.yml

When running the command without a mamba environment, using the python=3.6.8 from /usr/bin/python, I got a new error: link.

I also tried python=3.11.5 without a mamba env, and it gives the same error as above.

Could you help me take a look at these errors?

Thanks,
Nil

83

The latest issue seems to be that your hard drive is out of space - can you clear some space (I’d recommend having at least 15GB free), and try again?

You shouldn’t need to set up a conda/mamba environment in advance - you should just be able to use any python interpreter to run the fslinstaller.py script. FSL will set up its own conda environment(s) during installation.