Problem installing FSL

paulmccarthy · March 20, 2025, 4:08pm

Hi @Tiying, I’m afraid your OS is too old - Apple stopped supporting this OS over four years ago. You’ll have to upgrade your OS/machine*, or install an older version of FSL.

I’m on holiday at the moment, and don’t have access to a mac, so I’m not exactly sure what version of FSL will install on High Sierra, but you could try e.g.:

python fslinstaller.py -V 6.0.7

The full list of FSL releases can be found here.

Alternatively, if you don’t need the MIST sub-cortical segmentation tool, you may be able to install the latest version of FSL with a command such as:

python fslinstaller.py \
  --exclude_package fsl-mist \
  --exclude_package vtk-base \
  --exclude_package wxwidgets \
  --exclude_package wxpython

This command is untested, so there may be other dependencies that are not compatible with your OS. If the installation still fails, please share the log file and I can try and suggest an alternative.

You should not need to use the --conda option at all.

*You can blame Apple for this situation.

Tiying · March 22, 2025, 10:21am

Thank you very much Paul @paulmccarthy ! I will try to either upgrade my Mac system, or I will use the codes you suggested to download an old version FSL! Hope you have a nice holiday!

Tiying · March 31, 2025, 11:44pm

Hi @paulmccarthy , I tried to download, Version 6.0.5 was successfully downloaded. But in the process of installation, there is no progress in Stage 2, it always appear 1% and no change in two hours. I wonder if it is because my machine (Mac High Sierra 10.13.6) is too old, or other potential reasons? Can I please ask for some advice in this situation? Thank you so much. I attached the code:
Checking FSL package

[OK] File downloaded

Installing FSL software version 6.0.5.2…

FSL exists in the current location, would you like to keep a backup of the old version (N.B. You will not be able to use the old version)? [no]: no

We require your password to continue…

password:

[OK] FSL software installed.

Performing post install tasks

Checking for X11 windowing system (required for FSL GUIs).

[OK] X11 (required for GUIs) found

Stage 1

By installing this python distribution you agree to the license terms in

/usr/local/fsl/fslpython/LICENSE.txt

100%

Stage 2

1%

paulmccarthy · April 2, 2025, 10:18am

Hi @Tiying, did you try the command that I suggested, to get the latest version? It seems to be working for me:

python fslinstaller.py \
  --exclude_package fsl-mist \
  --exclude_package vtk-base \
  --exclude_package wxwidgets \
  --exclude_package wxpython

Tiying · April 2, 2025, 10:00pm

Hi @paulmccarthy I tried today and it finally downloaded and installed successfully. So happy to see the FSL interface working finally! Thank you for your help and making my day

pawel.szwajnoch · May 8, 2025, 11:31am

Hi guys, maybe it will help somebody with Linux (Ubuntu 24).
For me the file downloaded from here: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py worked perfectly when I run just python3 fslinstaller.py.

The issue I had:
This command returned an error: /home/ubuntu/fsl/bin/micromamba env update -p /home/ubuntu/fsl -f fsl-6.0.7.17_linux-64.yml --rc-file /home/ubuntu/fsl/.condarc

I fixed it by setting up a brand new machine with Ubuntu 22.04. It seems like the installer doesn’t work on Ubuntu 24.

paulmccarthy · May 8, 2025, 11:36am

Hi @pawel.szwajnoch, FSL can be installed just fine on Ubuntu 24.04 - there must be another reason as to why it was failing for you.

pawel.szwajnoch · May 9, 2025, 2:02pm

Hmm maybe but I’ve got the same error like the guys above (on an fresh clear VM so it’s hard to detect an issue on my end) and just changing the Ubuntu helped for me

paulmccarthy · May 12, 2025, 6:51pm

@pawel.szwajnoch If you can share the log file from a failed installation, then I can give further advice.

ibrwr · June 18, 2025, 1:00pm

Hi, I’m running into the following error using the fslinstaller.py when untarring the micromamba installer. Has anybody seen this before / know a solution? This happens when creating an apptainer container using this template Use FSL with Docker/Singularity but with Ubuntu 24.04 as base and using python3.

Any help is greatly appreciated.

There is no extra FSL component called truenet - ignoring
Downloading miniconda from https://anaconda.org/conda-forge/micromamba/2.1.0/download/linux-64/micromamba-2.1.0-0.tar.bz2...
1 / 4 [######################################################################################################################################################] 5.9 / 5.9 MB |
Installing conda at /usr/local/fsl...
2 / 4 [############################################################################                                                                            ] 50 / 100 % |

ERROR occurred during installation!
    This command returned an error: tar -x -f miniconda.sh -C /usr/local/fsl

Removing failed installation directory /usr/local/fsl

FSL installation failed!
[details="Summary"]
This text will be hidden
[/details]

paulmccarthy · June 18, 2025, 1:06pm

@ibrwr it’d help if you could share the log file, but my guess is that your container environment doesn’t have bzip2.

ibrwr · June 19, 2025, 3:21pm

Thanks for the fast reply, adding bzip2 indeed solved the problem!

JINGYUE_WANG · July 7, 2025, 3:14pm

Hi! I have been trying to install fsl for a few days now and nothing seems to work. It’s always stuck on 4/4.
For this I used python3 fslinstaller.py --miniconda conda | Anaconda.org forge/micromamba/2.0.5/download/osx-arm64/micromamba-2.0.5-0.tar.bz2

When I use curl -Ls https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/getfsl.sh | sh -s, it’s always stuck on different percentage of 4/4 for hours.

paulmccarthy · July 7, 2025, 3:45pm

Hi @JINGYUE_WANG, the installation process requires about 4-5 GB of software/data to be downloaded - are you able to use a faster internet connection?

JINGYUE_WANG · July 7, 2025, 6:55pm

Thank you for your reply! I tried to download it at different locations with different internet connections, but this is my current internet connection (which works okay for other installations). Also, it is often stuck at a certain percentage instead of being overall slow

paulmccarthy · July 8, 2025, 7:46am

Hi @JINGYUE_WANG, can you run the installer script with the --debug option and, when the installation hangs, copy the log file and upload it here? The installer prints path to the log file when it starts up: