FSL download stuck at 100%

Software Support
13

Hi everyone,

I am encountering the same issue on MacOS. The download is stuck at Installing FSL at 100%.

Thanks for the help!
Maxime

14

i also encounter with this problem, how can i fix it?

15

Hi @maxime8 and @DennisLu, can you please run the installer with the --debug flag, e.g. python fslinstaller.py --debug, and share the log file online?

16

Hi @paulmccarthy - I have the same problem. I ran it with the --debug flag. I’m also MacOS. I have the file in Google drive - how can I share with you?

Thanks!!

17

Hi @mhv, you can either paste the link to the file here, or send me a message through neurostars (click on my username, then click on the “Message” button).

18

I don’t see the “Message” button. Perhaps because I am new to the site?

19

Hello Paul, here’s my log file. fslinstaller_4s4pyhp9.log - Google Drive

I’ve been having the same issue, getting stuck at 100% for about 5 hours.

Edit: I’ve installed it successfully on windows10. For me, the solution was to use this command instead
python3 “/mnt/c/Users//Downloads/fslinstaller.py”

20

I use --debug flag, i successfully install in the ebug folder, when I try default installation then stuck at “Installing FSL into …” 100%

21

@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.

22

Hi, I’m experiencing the same issue: stuck at 100%.
Here’s my log file.
Any insight would be amazing thank you!

23

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.

24

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.

26

Just in case if any other have similar problem. I would like to provide another workaround that works for me.

  1. If you have miniconda/anaconda installed and launched by default. Deactivate conda by conda deactivate
  2. Then try again python3 fslinstaller.py
1 Like
27

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.yml

Removing 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?

28

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.

29

Thanks for the note @paulmccarthy ; here’s a box link to the logs I’ve tried with various iterations of python or conda etc:

https://cedars.box.com/s/kbvnv3cghx1af78kkgao6voal1i7td9b

30

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.

31

Unfortunately, both instances failed (logs are attached in the same directory above):

  • fsl_installation_20240123110116.log
  • fsl_installation_20240123110552.log
32

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
33

Would you also be able to share the contents of your conda configuration file, i.e.:

cat ~/.condarc