FSL download stuck at 100%

Summary of what happened:

I’m downloading FSL through fslinstaller.py on my terminal. The miniconda downloaded well but FSL is stuck at 100%.

Command used (and if a helper script was used, a link to the helper script or the command generated):

cd ~/Downloads
python fslinstaller.py


FSL installer version: 3.5.7

Environment (Docker, Singularity, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

1 Like

Hi @Chandra_Park, how long have you been waiting for? The final step can take some time on systems with anti-virus software.

Thanks for your reply @paulmccarthy. I probably have been waiting for a least several hours. I tried deleting and reinstalling it a couple of times but the same problem persists. I don’t have any anti-virus software running that I am aware of. I’m on MacOS if that is helpful.

Would you be able to run the installer script with the --debug option, e.g.:

python fslinstaller.py --debug

And let it run until it reaches 100% at the Installing FSL into ... step, then wait another 10 minutes, and then share the installer log file? The installer prints the path to the log file when it begins.

How would I be able to share the installer log file? I’m just a high school student, so I’m a beginner to this whole thing. Thanks.

I’m guessing it’s too large to add as an attachment here. You could use any file sharing service of your choice, such as dropbox, google drive, etc. If you don’t have access to such a service, I can arrange a place to which you will be able to upload the file.

If you can arrange a method in which I can do that it would be so great.

Having the same issue on Windows using the WSL option, been stuck at 100% at the “Installing FSL into…” step for 4 hours.

Hi @Nima_Hadidi, would you be able to run the installer with the --debug option as I suggested above, and share the log file? If you are unable to share the file via e.g. dropbox, then I will need your email address in order to set up a shared folder via my university’s sharepoint (I’m still waiting for Chandra to get back to me on that).

Hello @paulmccarthy. I also encountered the same problem, stucking at 100% at the “Installing FSL into…” step. Would you kindly help me check what went wrong?
The log file after --debug is in
FSL download stuck at 100% – Google Drive
Thank you!

Hmm, this looks like a different / new issue - the installation completed, but then an error occurred at the very end whilst trying to clean up temporary files.

Could you try re-running the installer script again? I’ve made some changes and released a new version - the installer will auto-update, so it will end up running the newest version.

It worked. Really appreciate your help!

Hi everyone,

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

Thanks for the help!

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

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?

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?


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).

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

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”

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