Problems installing FSL

[Joan_Carreras_Diaz]

Dear Eurostars,

I am trying to download and install FSL but I am having some difficulties. Once I have downloaded, the fslinstaller.py, I execute the code:
cd ~/Downloads
python fslinstaller.py

As it is being done in the Download and installation video.

The message I obtain is the following one:
FSL 6.0.7.6 selected for installation

**Where do you want to install FSL?**

Press enter to install to the default location [/Users/joancarrerasdz/fsl]

**FSL installation directory [/Users/joancarrerasdz/fsl]:**

Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.6_macos-64.yml...

**Installing FSL in /Users/joancarrerasdz/fsl**

Downloading miniconda from https://github.com/conda-forge/miniforge/releases/download/23.1.0-3/Mambaforge-23.1.0-3-MacOSX-x86_64.sh...

[#############################################################] 59.6 / 59.6 MB /

Installing miniconda at /Users/joancarrerasdz/fsl...

[################################################################] 100 / 100 % -

Installing FSL into /Users/joancarrerasdz/fsl...

[################################################################] 100 / 100 % \

**ERROR occurred during installation!**

This command returned an error: /Users/joancarrerasdz/fsl/bin/mamba env update -n base -f /private/var/folders/v3/6cj35d497rj1hq0k0rjpfmj40000gn/T/tmpxv8cvnlb/fsl-6.0.7.6_macos-64.yml

Removing failed installation directory /Users/joancarrerasdz/fsl

**FSL installation failed!**

**Please check the log file - it may contain some more information to help you diagnose the problem: /Users/joancarrerasdz/fsl_installation_20231221175704.log**

How could I solve that?

Thank you,
Joan

[Steven]

Hi @Joan_Carreras_Diaz,

Possible duplicate of FSL download stuck at 100% - #18 by mhv.

Perhaps you want to run with debug mode and follow up with the developers on that thread.

Best,
Steven

[paulmccarthy]

Hi @Joan_Carreras_Diaz, can you share the log file that is mentioned in the error message?

[Joan_Carreras_Diaz]

Yes, of course, I believe you are talking about this file. I have uploaded in .txt because I couldn’t do it using .log
fsl_installation_20231221175704.txt (836.3 KB)

[paulmccarthy]

This looks like some sort of issue with mamba, the package manager. Could you try re-running the installer with the --conda option, which will cause it to use conda instead of mamba? e.g.:

python fslinstaller.py --conda

P.S. @Steven I suspect that the other issue is simply due to the installation taking longer than people expect as, despite it being reported numerous times, nobody has actually provided me with any further information (the few people who did provide me with a log file were affected by other issues).

[Steven]

Mamba has been experiencing compatibility issues with conda recently, so that makes sense.

[Joan_Carreras_Diaz]

Well, I am not stuck in this part but after 10 minutes on the 100% in the Installing FSL into part , it appears the error message.

[paulmccarthy]

Hi @Joan_Carreras_Diaz it looks like you didn’t add the --conda option? I suspect it will have failed for the same reason as before.

[Joan_Carreras_Diaz]

Hi, I have executed the line you have told me:

python fslinstaller.py --conda

But it does not seem to work. It has been in the 10% of the loading for more than an hour as you can see below. Is that normal?

Thank you,
Joan

[paulmccarthy]

When using the --conda option, I would expect the installation to take a bit longer, as conda is typically much slower than mamba.

[Joan_Carreras_Diaz]

Hi, I am still not able to install FSL, when using conda, it keeps stuck in the 10% of the installation as I have shown it before.

[paulmccarthy]

Yes, using the --conda option causes the installation to take a very long time for me. Does your macbook have a M1/M2/M3 processor by any chance?

edit: On my intel macbook when using --conda, the installation does eventually succeed, but is stuck at 10% for over two hours. This is because conda is much slower than mamba at solving the environment specification.

[Joan_Carreras_Diaz]

It is an intel processor. Do I need to wait about two hours and see if the installation completes?

[Joan_Carreras_Diaz]

Hi, after the 40% of the installation, it appeared the following error message.

I am trying to install onda but it does not seem to exist, as you can see below:

Thank you,
Joan

[Joan_Carreras_Diaz]

I have installed ondir as it was said in the Warning message. After that, I have tried again to install the FSL. This time, I had to wait two hours and a half and the installation stopped on the 71%.

[paulmccarthy]

Are you able to use a faster internet connection for the installation? The installation needs to download about 4GB of data, and can fail when attempted over poorer connections.

P.S. The ‘onda’ / ‘ondir’ packages are unrelated - the fslinstaller script only requires a python interpreter - I’m fairly sure that the installation is failing due to an unreliable network connection./

[Joan_Carreras_Diaz]

Yes, I have finally managed to download it. At the end I managed to get a wire and I tried using that. Finally I have succeeded.

Thank you, very much!
Joan

[aymen_meddeb]

Dear Paul,

I just bought an Macbook M3 Max and I have troubles installing FSL
Here is the error:

[paulmccarthy]

Are you able to share the log file that is mentioned? This is probably due to an issue with mamba which is still outstanding, and which can hopefully be avoided by running the installer script with the --conda option, e.g.:

python fslinstaller.py --conda

[aymen_meddeb]

Dear Paul,
obviously there was an env conflict in my base, I resolved the problem with creating a new env dedicated for fsl, then it worked,
Thank you so much!!
Best,
Aymen