Hi Paul,
When I went to go and download the unix dataset for practice from the website, the response was this:
Hello, I recently purchased a new MacBook Air (M3, Sonoma 14.4.1) and have tried to install FSL with no success (I have installed FSL on previous machines with no problem). The “Installing FSL into …” step keeps stalling at 93%, and then I get the following error:
ERROR occurred during installation!
This command returned an error: /Users/User/fsl/bin/conda env
update -p /Users/User/fsl -f /private/var/folders/hh/p779zgr17tb91xm578k
k0lwc0000gn/T/tmpij_787a2/fsl-6.0.7.11_macos-64.yml
Removing failed installation directory /Users/User/fsl
FSL installation failed!
Please check the log file - it may contain some more information to
help you diagnose the problem:
/Users/User/fsl_installation_20240514010933.log
I’ve tried downloading the installer from the link recently supplied, and ran the command that seem to work for others (python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh), but no success. Any suggestions?
I did, but unfortunately don’t understand it. Can access the log here in case it’s helpful (won’t let me paste)?: Dropbox - fsl_installation_20240514010933.log - Simplify your life
Are you able to share a copy of the log file where you ran fslinstaller.py without any additional arguments? Passing an alternate miniconda installer should no longer be necessary.
Hi @David_F, actually I think there has been a change to conda which has broken FSL installations. Can you try re-running the fslinstaller.py script like this (don’t specify an alternative miniconda installer):
CONDA_AUTO_UPDATE_CONDA=false ./fslinstaller.py
and see if that allows the installation to succeed?
I get a permissions issue with that:
zsh: permission denied: ./fslinstaller.py
Am I missing something simple?
Sorry, I meant something like the following (using whatever python you used to run the installer previously):
CONDA_AUTO_UPDATE_CONDA=false python ./fslinstaller.py
That works, thank you!
1 Like
keep getting this error…tried solving it with some suggestions I found online but nothing seems to work
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
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?
As a new user I apparently cannot upload files. Can I send it to you in another way?
Do you have access to a file sharing service, e.g. dropbox, google drive, etc?
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
Does this link work for you? 
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
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
@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