Problem installing FSL

Hello,
I have troubles installing FSL on my MacBook Air M2, OS Sequoia 15.2
I downloaded the flinstaller.py that i compiled in my terminal using python/python3, either in my downloads file or a Users/myname/softwares/ repository i created
I keep getting stuck at the 3rd step of installation : Installing FSL into /Users/asavalle/softwares/fsl/v…
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i get a similar error message each time, no matter the conda environment with good version of python, or the repository, or using --conda or not. Is there anything i could do ?
as i cannot add any attachment file bc i am a new user, here are 2 screenshots of the last lines of the log file :


Thank you in advance for your help and answers

Hi @adele, are you able to share the installer log file by some other means, e.g. dropbox, onedrive, etc?

Hi @paulmccarthy, here is a folder with some of the logs I got, either using conda or not, installing in a specific folder or not : FSL log

Hi @adele, you might have suc?cess by trying a different conda installer - could you try using miniforge, e.g.:

python fslinstaller.py --miniconda https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh

Hey @paulmccarthy sorry for this late answer. Thank you for your answer.
I tried installing fsl with the command you gave me, and then with miniconda installed directly on my computer, also tried using conda, and using advices given in : Problems installing FSL - #30 by Tru_Gamble such as doing the installation in a created conda environment.
I always end up with the same problem : the 3rd step of installation stuck at 0% and an error message with the log file mentioning "/Users/asavalle/Dev/fsl/bin/conda env update -p /Users/asavalle/Dev/fsl -f fsl-6.0.7.16_macos-M1.yml . ". I have no trace of this yml file, maybe there is something i could do there ? Thank you in advance for your help

Hi @adele, would you be able to share the log file that is saved when you run the command I suggested in my previous post?

Hi @paulmccarthy here is the log file fsl_installation_20241230150809.log

Hi @adele, sorry for the delay. Could you try re-downloading the fslinstaller.py script, and running it like so:

python fslinstaller.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2

I’ve updated the installation script to allow FSL to be installed with micromamba, which will hopefully resolve the conflicts you are experiencing.

Hi @paulmccarthy, I tried 2 co;;ands with this new flinstallerfile, and both failed, here are the fsl logs associated to each one :
python fslinstaller.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2 gave fsl_installation_20250113091541.log
python fslinstaller.py --micromamba https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2 gave fsl_installation_20250113093230.log
Thank you really much for your help !

Hi @adele, I’ve fixed a bug in the script - can you re-download it again, and try running the command from my previous message? The flag is --miniconda, not --micromamba.

Hi, this is what I got this time : fsl_installation_20250113110125.log

@adele Sorry, my mistake - I accidentally pasted the URL to the linux installer. Can you try this:

python fslinstaller3.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/osx-arm64/micromamba-2.0.5-0.tar.bz2

Capture d’écran 2025-01-13 à 13.36.03
yayy thank you very much for your help and your time !

1 Like

For posterity, we will be soon be switching to micromamba by default, at which point it will not be necessary to pass the URL to a specific micromamba installer.

Hi.
I finally managed to install fsl 6.0.7.16 on a Rocky linux cluster using this method. I used FSL installer version: 3.16.3. However, it did not work when I tried installing it with -e truenet, just worked without it.

I am also unable to add truenet with update_fsl_release --extra truenet (adding --cuda 12.1 or not adding it did not change the outcome). it complained about not finding conda or mamba executables in $FSLDIR/bin. I symlinked micromamba which was there as mamba but then it just fails
without complaining about conda/mamba.

File “/work//fsl/lib/python3.12/site-packages/fsl/installer/fslinstaller.py”, line 1343, in monitor_progress
raise RuntimeError('This command returned ’
RuntimeError: This command returned an error: /work/zhang_lab/Shayan/fsl/bin/mamba env create -p /work//fsl/envs/truenet -f fsl-6.0.7.16_truenet_linux-64.yml

adding --miniconda as suggested above to fsl_update_release or fslinstaller.py was not was not helpful either for truenet.

@paulmccarthy Thank you!

Hi @shneuro, your timing is slightly unfortunate - I have added preliminary support for micromamba to the fslinstaller.py script, but the update_fsl_release command does not yet support micromamba. Can I ask what issues you were encountering when running the fslinstaller.py command normally (i.e. without --miniconda <url>)?

@paulmccarthy It just does not install. please check the screenshot.
The command was python fslinstaller.py -r

Hey @paulmccarthy – I’m having a similar problem and I’ve tried the fixes in this thread. Any suggestions? I’m on Mac OS 15.2. I cannot upload the log but got an error at Stage 4 (pasted below). Thanks!

ERROR occurred during installation!

This command returned an error: /Users/CHOIKX9/fsl/bin/conda env update

-p /Users/CHOIKX9/fsl -f fsl-6.0.7.16_macos-M1.yml

Removing failed installation directory /Users/CHOIKX9/fsl

FSL installation failed!

Please check the log file - it may contain some more information to

help you diagnose the problem:

/Users/CHOIKX9/fsl_installation_20250120234223.log

@shneuro @ypathak I really need to be able to see your log file to help. If you can’t upload it here, you can use any file sharing service of your choice (dropbox, google drive, onedrive, etc).

@paulmccarthy Here is my log file.
https://www.dropbox.com/scl/fi/tq0za4r6uvhe3u0sw5drj/fslinstaller_rwNhAK.txt?rlkey=at32c07bfd4an7lxf5m6lmd7l&st=lcelcaol&dl=0