@Sam_Min so was that log file from the attempt that hung for 5 hours? The log file implies that the download failed after about 10 minutes due to a connectivity issue.
Hi, I’m experiencing the same issue: stuck at 100%.
Here’s my log file.
Any insight would be amazing thank you!
Hi @sosun, this looks like a different issue (it looks to me like the installation failed, rather than getting stuck). Can you try re-running the installer script with the --conda option, e.g.:
python fslinstaller.py --conda
to see if that resolves the issue? Note that it will take up to an hour longer, as conda is much slower than mamba.
It worked, thank you so much!
It got stuck at 10% for a couple of hours, but I just waited it out and then it successfully installed.
Just in case if any other have similar problem. I would like to provide another workaround that works for me.
- If you have miniconda/anaconda installed and launched by default. Deactivate conda by
conda deactivate - Then try again
python3 fslinstaller.py
1 Like
Hi Paul;
I’ve tried all suggestions in this thread and either it will hang at 100% or fail outright (I cannot attach logs, but the last lines are similar to others:
Downloading miniconda from https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Mambaforge-23.11.0-0-MacOSX-x86_64.sh…
[#########################################################################################################] 58.6 / 58.6 MB /
Installing miniconda at /usr/local/fsl…
[############################################################################################################] 100 / 100 % /
Installing FSL into /usr/local/fsl…
[############################################################################################################] 100 / 100 % \ERROR occurred during installation!
This command returned an error: /usr/local/fsl/bin/mamba env update -n base -f /private/var/folders/5z/5rzkyvn571x85jvybvb73kgr0000gy/T/tmpp557fdem/fsl-6.0.7.7_macos-64.ymlRemoving failed installation directory /usr/local/fsl
FSL installation failed!
Please check the log file - it may contain some more information to help you diagnose the problem: /Users/rennermd/fsl_installation_20240117114446.log
Running macOS 14.2.1, MBP 2020 16". Any ideas?
Hi @RennerMD, I really need to see the log file in order to help. There are a plethora of methods for sharing files online. e.g. dropbox, google drive, sharepoint, etc.
Thanks for the note @paulmccarthy ; here’s a box link to the logs I’ve tried with various iterations of python or conda etc:
Would you be able to try installing FSL with an alternative miniconda installer, by running this command?
python fslinstaller.py --miniconda https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Miniforge3-23.11.0-0-MacOSX-arm64.sh
If it fails, try running it again with the --conda option.
Unfortunately, both instances failed (logs are attached in the same directory above):
- fsl_installation_20240123110116.log
- fsl_installation_20240123110552.log
Sorry, oversight on my part - you’re using an intel mac. Can you try this:
python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
Would you also be able to share the contents of your conda configuration file, i.e.:
cat ~/.condarc
Excellent! This seems to have installed it… Thank you, Paul!
Was it just a repo issue from the download script?
→ cat ~/.condarc
solver: libmamba
Hello, I am having the same issues and I’ve tried all the alternatives this and other discussions suggest. I think this is the error from the log file that is causing the issues (see below), and it might be a compatibility issue ? I have a Mac M2 with Sonoma software. I’ve already tried the -conda version and the python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh but this just stays at 0%…
ERROR occurred during installation!
16:32:20 fslinstaller.py: 206: This command returned an error: /Users/adefen/fsl/bin/conda env update -p /Users/adefen/fsl -f /private/var/folders/w8/t8b01qxx1r9gsl5_mxj1dz_80000gn/T/tmpctiwqaeq/fsl-6.0.7.7_macos-M1.yml
Hi @stef_d
Going by the information you gave at FSL not downloading properly, you should be able to resolve this by downloading and running an updated version of the fslinstaller.py script from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py. You shouldn’t need to provide any additional options, e.g. --conda or --minicopnda. When you run the installer, it should say that it is version 3.8.2
Hello, thank you. Sadly, this doesn’t work and gives the same error. I am unable to upload an attachment as a new user but here is the error :
Downloading miniconda from https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Mambaforge-23.11.0-0-MacOSX-arm64.sh..[#############################################################] 55.7 / 55.7 MB -
Installing miniconda at /Users/adefen/fsl...
[################################################################] 100 / 100 % \
Installing FSL into /Users/adefen/fsl...
[############################################################ ] 92 / 100 % -
**ERROR occurred during installation!**
This command returned an error: /Users/adefen/fsl/bin/mamba env update-p /Users/adefen/fsl -f /private/var/folders/w8/t8b01qxx1r9gsl5_mxj1dz_80000gn/T/tmpcg3uwj9w/fsl-6.0.7.7_macos-M1.yml
Removing failed installation directory /Users/adefen/fsl
Restoring contents of /Users/adefen/fsl
**FSL installation failed!**
**Please check the log file - it may contain some more information to**
**help you diagnose the problem: /Users/adefen/fsl_installation_20240206172116.log**
And from the Log :
16:32:20 fslinstaller.py: 206: This command returned an error: /Users/adefen/fsl/bin/conda env update -p /Users/adefen/fsl -f /private/var/folders/w8/t8b01qxx1r9gsl5_mxj1dz_80000gn/T/tmpctiwqaeq/fsl-6.0.7.7_macos-M1.yml
16:32:20 fslinstaller.py:2710: File "/Users/adefen/Downloads/fslinstaller.py", line 2702, in handle_error
yield
File "/Users/adefen/Downloads/fslinstaller.py", line 2816, in main
install_fsl(ctx)
File "/Users/adefen/Downloads/fslinstaller.py", line 2096, in install_fsl
ctx.run(Process.monitor_progress, cmd, env={'CONDARC' : condarc},
File "/Users/adefen/Downloads/fslinstaller.py", line 1553, in run
return process_func(admin=self.need_admin,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/adefen/Downloads/fslinstaller.py", line 1024, in monitor_progress
raise RuntimeError('This command returned '
Sorry, I need to see the log file in order to advise further - you can use e.g. google drive, dropbox, onedrive, etc.
thanks, here is the link : https://drive.google.com/file/d/10YVqOAlUEumpI71ak21PcNx-FCpjzHg_/view?usp=sharing
Ok, you are being affected by an issue that is still outstanding (I don’t have access to a Sonoma machine, so have been unable to reproduce or diagnose it). There are a couple of things that you can try:
-
Run the fslinstaller with a different python interpreter - it looks like you are using
~/anaconda3/bin/python, but you could try running the fslinstaller like this instead:
/Library/Frameworks/Python.framework/Versions/3.12/bin/python fslinstaller.py -
Tell the fslinstaller to use a different miniconda environment - some people have reported success when running:
python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh